I've flown with my daughter many times...don't worry...you'll both do great and it's only temporary! Here's a few suggestions that have made flying with my daughter much easier. When you check in, ask if it's a full flight. If it isn't a full flight usually you can be moved around so that your son can have a seat (I always double check at the gate as well...just in case someone didn't show up last minute) I prepare her and tell her she will need to sit in the stroller while we stand in lines. I tell her that after we go through security (and I explain what that is) if she can hold my hand or the stroller she may walk by me. This does make things a bit slower and I'm always paranoid while she's walking, but it helps her burn off energy and makes it so she isn't sitting the whole day.
The second thing I do is have 2 sets of play things. One for the airport and one set for the plane. The airport toys are toys that keep her occupied playing on the floor in a confined area, but she can still move around. Things my daughter likes are her little people and a few cars to drive around. I try to sit on a chair right by the window and give her boundaries she has to stay within on the floor.
Toys for the plane that have been amazingly great for us are color wonder markers, a small aquadoodle and some of her favorite books and comfort items. Once the fasten seat belt sign is off I let her stand in between my legs. (If you can't get an extra seat for your son, sitting in the first row is also helpful b/c there is a little more floor room...you just have to store your bags above.)
The third tip...pack lots of yummy snacks. I never worry about nutrition on travel days...whatever she'll eat and whenever is great. I allow her special juice I buy once past security and I pack fruit leathers and other fun treats she doesn't usually get. All of these things make time go by quicker than you'll realize. Also, make sure you prepare yourself for realistic expectations...continue to encourage and praise him for behaving and don't get to frustrated if he's antsy or cranky...travel is stressful for them too!
Also, if you are flying during naptime I find it's helpful to talk about how when the plane takes off he will cuddle on mommy's lap and take a nap NUMEROUS times. I've found that the times I've talked about that ahead of time she's just curled in and taken a nap once we take off but if we didn't talk about it ahead of time she can't quite fall asleep.
Good Luck and Have Fun!! If it's an aweful day just remember "this too shall pass"