Unless you just want to get a lot of pictures of the backs of people's heads, you're going to want to be in a window seat.
Don't put anything in your checked luggage that you can't afford to lose. Even if 99% of the airline/airport employees are honest, a good camera is still too juicy a target for thieves to pass up. And even if nothing is stolen, unless you've really got that thing packed securely - the way they toss those bags around is asking for something to be broken.
Don't worry about having a lot of different equipment with you in your seat. There's not going to be a lot of room for you to change lenses etc., and too great a chance of dropping something and losing it.
I hope your seats aren't over the wings. Otherwise you're going to have to be taking your pictures at a fairly steep angle with respect to the plane, and you'll probably get too much distortion from the windows to get a good picture.
Your best bet is probably going to be aiming from about 30 degrees away from straight down to about 60 degrees (and a similar range forward or back - depending on wings and engines). If you try to get a picture of something too close to straight below you you're going to get too much window distortion. Too far away and you're not going to get much detail.
The best shots are probably going to be available during the first and last twenty minutes of the flight, while you're still low enough to see a lot of detail.
Don't expect a lot of great shots. Things are going to be too far away and pass by too fast. (Those pictures that do come from flying are generally taken by people who know in advance what's coming, and who have some input into where the pilot goes and how he gets there. You're just going along for the ride.)
Don't forget to look around at your level and above, and in front and behind you. You can often see other aircraft flying by, and that can make for an interesting shot (it's an unusual perspective for most people).
If you're actually in clouds (most likely at the start and end of the flight) all you'll be able to get is a white or gray blur. Once you get above them, though, don't think that your picture opportunities have been ruined. Look for interesting patterns in the clouds (sometimes it looks like they have canyons in them). This time of year in that part of the country, you might even see thunderclouds off in the distance.
