When ATC and GPS Don't Agree

So there you are with your cool and classy "Instrument Airplane" rating on your Pilot Certificate, and access to a nice plane with the latest whiz-bang Global Positioning System (GPS) navigator approved for Instrument Flight Rules (IFR). Before you head into the clouds there are a few things you probably ought to know how to do with the GPS unit. The problem is that the usual training aids like user manuals and such tend to be a bit heavy on the details like what's on AUX page 15 and which buttons to press to initiate RAIM prediction but somewhat short on how to respond when ATC tosses you a curve ball when you're bouncing around in the soup.
After several years of teaching and flying a variety of GPS units, I have noticed that there are certain situations that come up which seem to be difficult for pilots, even those who have carefully studied the manuals and practiced with the boxes. I've listed many of those situations here so pilots can think about how to handle them during ground-based comfort instead of during airborn panic.

I also hope this list will be helpful to pilots starting to learn a new GPS by answering "what do I need to know in order to fly this thing under IFR?"

Please notice that while I list the situations (and examples) I do not talk about techniques for handling each situation, or specific models of GPS. There are often several valid ways to deal with a given task, and I may later add some info on how I do these tasks for various models of GPS, but mostly you want to use this list as a way of testing yourself.

Of course, this is offerred as the opinion of the author (me), and you should use your own brain to think about it. Do not follow anything said here blindly, and especially don't sue me if you do.

On the other hand, if you would like help improving your skills using your GPS, please consider hiring me! :-)

Note: I haven't found a stable reference for the approach plates, but clicking on the airport name will take you to Airnav where you'll be able to view the current plate.
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The Basics

Situation: Enter and activate a flight plan (Bonus: can you store it and later call it up for resuse to make your life easier?)
Example: The typical routing from Palo Alto (KPAO) to Stockton (KSCK) is "...Radar Vectors SJC, V334, SUNOL, V195, ECA, Direct", which becomes this route for the flight plan: KPAO SJC SUNOL ECA KSCK
Situation: Navigate Direct to a waypoint in the flight plan.
Example: Assuming the flight plan given above, from south of SUNOL: "Proceed direct Manteca"
Situation: Direct to waypoint not in flight plan.
Example: Assuming the flight plan given above, from near SUNOL: "Proceed direct TRACY" (note that TRACY is on the route from SUNOL to ECA (V195), but doesn't have to be in the flight plan since there is no turn required there)
Situation: Does setting a Localizer (LOC) frequency override GPS selection on the Course Deviation Indicator (CDI)?
Example: Set up any GPS flight plan and begin navigating with it. Select a LOC frequency on the nav receiver that shares the CDI with the GPS. Does the CDI switch to showing the LOC signal or stay on the GPS? (Note that the same equipment can often be installed to either override the GPS when a LOC is tuned or not, so you should check this in every new airplane you get into, even if it has equipment similar to ones you are already familiar with.)​​​​​​​
Situation: Setup and fly NoPT approach from IAF or transition fix.
(this includes understanding CDI scale changes and what to do at the Missed Approach Point (MAP))​​​​​​​
Example: You're over Manteca (ECA) heading to Livermore (KLVK), cleared Direct TRACY: "Cross TRACY at 3,000', Cleared for the GPS 25R approach to Livermore." What do you do with the GPS after RW25R? When exactly is the right time to do that?
Situation: Setup and fly an approach with vectors to the final approach course.
Example: After vectors to 3 miles SE of IPDEW: "3 miles from IPDEW, turn left heading 260, intercept the final approach course, maintain 2,000' until estabilshed, cleared for the GPS 29R approach to Stockton."
Situation: Setup and fly an approach with Direct to a non-IAF fix in the approach procedure.
Example: Enroute KPAO, expecting the GPS 31, you get "proceed direct DOCAL" then later "Cross DOCAL at 4,500', cleared GPS 31 approach to Palo Alto." (Note that DOCAL is not an IAF.)
Situation: Hold at Missed Approach Holding Point (MAHP).
Example: Almost any approach will do, but you must fly the approach and go missed. The GPS-A into Tracy (KTCY) is a good example.
Situation: Setup and fly published Standard Terminal Arrivals (STAR).
Example: You are enroute to Fresno. The ATIS is reporting runways 29 in use. Your clearance is "...VIS, Altta Seven Arrival".
Situation: Setup and fly published Departure Procedures (DP).
Example: Your clearance out of Santa Rosa (KSTS) is "Frees Six Departure, Mendocino transition, ..." (Can you fly the holding pattern at FREES, too?)
Situation: Intercept route after vectors when GPS isn't "on" the correct leg.
Example: You've loaded in the route given above for KPAO-KSCK. After departing PAO the GPS is "on" the KPAO to SJC leg. You get vectors to southwest of SUNOL (but not so close to SJC that the GPS steps to the SJC-SUNOL leg), and then: "Fly heading 040, intercept victor 334, resume own navigation"

The Trickier Bits

Situation: Enroute hold.
Example: You're on a leg from SUNOL to ECA, planning to approach at KSCK, but they have a temporary problem and need you to wait: "Hold north of ECA on the 010 radial, maintain 4,000, expect further clearance ..."
Situation: Correctly fly Procedure Turn (PT) or Hold-in-lieu-of-PT.
Example: KSCK GPS 29R starting from ECA. (PT is rare on GPS-only approaches, but common on ILS & VOR approaches where GPS can be used for non-FAC guidance.)
Situation: Hold in Hold-in-lieu-of-PT for more than one turn.
Example: You're Approaching OXJEF from ECA on the KSCK GPS 29R and you get "I've got an aircraft in distress I need to put in front of you. Hold east of OXJEF as published, maintain 3,000', expect further clearance in 10 minutes." Or you find you're too high and ask for another turn in the hold to loose some altitude. How do you set up your GPS to stay in the hold?
Situation: Flying different kinds of missed approaches.
Example: Distinguish between how the missed is flown in the SCK GPS 29R versus LODI GPS-A or SCK NDB 29R
Situation: Getting guidance after an early missed approach.
Example: You're on the GPS 25R @ LVK. Before reaching the MAP (RW25R) ATC tells you to start your missed approach turn now.
Situation: Setup for next approach when holding at MAHP.
Example: After flying KSNS GPS 13 you miss and hold as published at MARNA. While doing that, set up for the KMRY GPS 10L
Situation: Load an approach for a new airport when another is in the flight plan.
Example: You're enroute to KSCK with the approach all set up when ATC tells you KSCK is closed. You need to divert to KLVK and shoot the GPS 25R approach.
Situation: A strange message pops up on the GPS screen, like "Approach not active" or "RAIM failure". What does it mean and what do you do?
Example: See the list of messages given in the manual. For each one, imagine yourself flying along and getting that message. What will you do?
Situation: Fly an approach when all the fixes used aren't in the database. (This is becoming more rare as the powers-that-be realize it was a mistake, but for approaches with step-down fixes inside the FAF those fixes are sometimes not in the databases, especially on older units)​​​​​​​
Example: Fixes inside the FAF on KHWD GPS 28L
Situation: When the approach isn't in the database (Of course, this only applies to units that have non-GPS approches in the database. As far as I know it only happens when there is more than one localizer-type approach to a given runway (2 ILS, 2 LDA, etc.))
Example: Try to fly Arcata's (KACV) ILS 32 and ILS/DME 32 or South Lake Tahoe's (KTVL) LDA/DME-1 RWY 18 and LDA/DME-2 RWY 18. (Do you know why KTVL has 2 LDA procedures? Hint: deep snow tends to block VHF radio waves.)
Situation: Change the procedure late in the game.
Example: You're on the way to KSCK, expecting the GPS 29R. You load the approach with the transition from STLLR. Then ATC tosses you the curve: "Proceed direct OXJEF, cross OXJEF at 2,000', cleared for the GPS 29R approach to Stockton". You need to reset the approach to get the course reversal at OXJEF.
Situation: Using "vectors" mode: are you joining the final approach course, or the published approach outside the FAF?
Example: You're approaching San Jose on the way to KPAO, expecting the GPS 31 approach. You select "vectors" mode. You get "Fly heading 270, vectors for the approach" and then later "You are 4 miles from PUDBY, fly heading 300, join the approach, cleared for the GPS 31 approach to Palo Alto...." Or possibly you get "join the final approach course". What do you do? What guidance are you getting from your GPS (final approach course (329) or published approach (322))? (This is a fairly trivial example, but you may run into situations with lager differences between the FAC and the published approach outside the FAF, so you want to know what will happen and how you'll handle it.)
Situation: Using "vectors" mode: a last minute "Direct-to" a fix outside the FAF.
Example: You're approaching San Jose on the way to KPAO, expecting the GPS 31 approach. You select "vectors" mode. You then get "Proceed direct DOCAL and join the approach, ..." (When using vectors mode, is DOCAL in your flight plan? Many GPS models with "vectors" modes drop all the fixes outside the FAF from the flight plan when "vectors" are used. Before GPS, ATC would generally give either vectors to the Final Approach Course (FAC), usually to a point just outside the Final Approach Fix (FAF), or route you over an Initial Approach Fix (IAF). With the GPS approaches it is much more common to get vectors to an intermediate leg that is not quite the FAC but not over an IAF either. This can generally work well, but you need to be careful when you join the approach well outside the FAF. Are there stepdown fixes between you and the FAF? Are the FAC and the leg you are joining really the same?)
Situation: Skip or remove a flight plan waypoint.
Example: You're on the way to VINCO flying KPAO VINCO CATHE MOD and get "after VINCO, proceed direct MOD."
Situation: Add additional waypoint(s) to the active flight plan
Example: You're flying VINCO PXN AVE and get "after PXN, Victor 113, ROM, Victor 137, AVE, then as previously cleared." You need to add ROM to the flight plan after PXN.
Situation: Fly approaches with DME arcs.
Example: You're crossing SHOEY on V230 on the way to Watsonville (KWVI). You get "Cross JEJZE at 3,200, cleared for the GPS-A approach to Watsonville."