I flew up to Boston to see my parents when Oliver was a baby. It was 2 years ago, so I am trying to remember the particulars...but it went smoothly and that flight was about 2 and a half hours. He went in a carrier under my seat. I actually did take him out and let him snuggle in a blanket on my lap...but you have to be careful that your neighbors and the flight crew don't mind (and aren't allergic), as you are really not allowed to do this. He slept the whole way.
As for pottying, I didn't give him food or water before we went (at the vet's advice)- I would check with your vet. I took him outside of the airport to potty when I first got to it and again when we landed.
The hardest part was juggling everything since I was by myself, but I am sure it will be easier for you with another person.
Holly, Oliver, Rosalita, and Scarlett