I just did the AIA marathon on Saturday. Part 1 goes by very quickly and comfort wasn't a major issue (at least no more than most other theatre experiences can be with the generally standard poor leg room), but by the end of Part 2, which gets a little weird, it got to be a bit of a struggle. It doesn't seem like much but that extra 20-30 minutes makes a difference - the first two acts are longer too, which doesn't help that feeling. Act III was maybe about 50 minutes or so?
All that said, it was a very neat experience to do all of that in one day. I think it also helps you notice the different growth arcs that nearly all of the characters embark on. Also, even one part is a big commitment so why not go all out? As long as you understand what you're in for, I think you'll find that ultimately it was worth it. Sleep in a bit that morning, stretch your legs during intermission, and stay away from alcohol until after the show.