I flew to pick up Izzie when she was 12 weeks. She did great...other than the fact she was a little scared from being separated and with a stranger. I don't think the cabin pressure bothered her ears. We also had a layover in SF for a couple of hours. I took a pee pad, some water, a little food, toys, and some nutri-cal. We just found a 'quiet' corner and set up a little area and played and got to know eachother. Other than people wanting to pet and hold her it was fine.
During the flight the only time she was under the seat was on take off and landing. They let me hold her on my lap during one leg of the flight, but on the other the flight attendant let me hold the carrier on my lap, but not take her out. Something about people's allergies
I wasn't sure what the difference was if she was in my lap or in the carrier.
I'm sure you will do fine. Make sure you don't carry too much...not easy with a bunch of bags and a pup too.