Cissy (now 8 mos.) and I traveled on an American Airlines 3 hr flight in Dec. We too used the Kwigy Bo Alex bag. After reading the advise in the YT Travel Section, this is what we did -
We did get our health certificate, although no one asked for it, we were prepared "just in case". I did not want to give a sedative and the vet suggested giving her a little Benadryl about 1 hr before the flight. After reading about some dogs panting on the flight, I also took a little hand held fan which I could put in front of the vent on her bag and just held it in between my feet so she was getting good air circulation. I also took her a toy, treat and a hand towel in case. I got her a little water from the flight attendent. I had also read that her experience on the flight would depend on the airline staff, which I can confirm. On the flight out, the attendent offered us two empty side by side seats so Cissy would be more comfortable. She told me she "just loved dogs". The only time Cissy was under the seat was during take off and landing, although she did stay in her bag, it was on the seat unzipped and she had her head out laying on the bag sleeping. On the return flight it was just the opposite, I had Cissy in her bag on my lap and the attendent was very upset with me, I had to "keep the bag zipped closed and under the seat". Even the passengers around us were upset because Cissy was causing NO problems, but as she said - rules are rules! So it definately depends on the flight attendent. The return trip was when I did use the fan and she did just fine. At the airports, I would put her unzipped bag in my lap and she was the hit of the airport, if anyone noticed they wanted to come see her.
She was better than I anticipated.
Sorry for the long post but I was a nervous wreck before the flight and I am trying to relieve some of your worry. Cissy did fine on both legs of the flight even though they were totally different experiences. Hope this helps a little. Good luck!