We did AP in August and both DW and I had the wine flights with our meals. Our server made suggestions, but the choice is up to you. However, our server was excellent, so she wound up bringing us samples of four different wines from which we were trying to choose--no charge. Being an accomplished oenophile (though nowhere near an expert), I have found that most top tier restaurants will give you free samples if you ask, since the mark up on wines in most restaurants is anywhere from 100-200% over retail, so if you wind up ordering wine, that's a big profit leader for them. Thus, a small sample or two or three won't hurt the bottom line.
In my particular case, I chose to have a glass of a lighter red for my appetizer and salad courses, a glass of hearty red for my entree, and a glass port to go with my dessert. When I ordered my port, I expressed some indecision between it and another, so when dessert came, I got my glass of port plus a sample of the one I did not choose. As you might imagine, we tipped our server quite well, as she made our dinner an exceptional experience.
Keep in mind for the flights that you can order three glasses of the same wine if you wish, or you can order three different glasses. Once again, I'd urge you to ask for a couple of samples unless you have complete confidence in your server's opinion. As for which wine to order with which course, that takes years of expererience, and I'm still learning. As a general rule, however, lighter wines (most whites, pinot noirs, and some merlots), go with lighter foods, while heavier wines (zinfandel, some merlots, cabernet sauvignon) pair up better with more substantial fare such as filet or steak. Above all else, go with what you like. Bon appetit!