When my son was young, I traveled with him on my own from Maryland to Washington State several times a year. I used his car seat with tremendous success every time. If you do not already do so, I would highly recommend always putting him in the window seat. This isolates him from others on the plane and makes the things going on around him less interesting. The worst flight I ever took with my son was when he was two - he was very verbal and VERY curious. We were on a large plane with 5 seats across the middle - we had the aisle seat and the next seat in. A woman sat down in the middle seat - the seat on her other side was empty. I suggested to her that she might want to take advantage of the empty seat to which she replied, "this is my seat and I see no reason to change." When she was glaring at my son midway through the flight because he kept taking her pen, trying to write in her daytimer, was asking a million questions about her book, I figured she got what was coming to her. :) I did not want to put him on the aisle because I was afraid he would stick his hands out when people and/or carts went by.
The other thing I have learned in flying long distances with my kids is to try and fly at night whenever possible and to be armed with Triaminic (it helps if their ears clog up and it helps make them drowsy - sleeping on the plane is always a good thing).
Finally, I always pack a BIG bag of *stuff* for my kids. I was once told by a parent to pack a bag of goodies that they have never seen before - nothing big, just stuff from the Dollar Store...when they start getting restless, give them something new and fun to get their attention.
When my kids were 2.5, 4 & 9 we traveled from PA to Hawaii (almost 14 hours in the air). All of the above worked wonders for us. We did invest in a really comfortable car seat with deep sides for our youngest - it was worth the investment for the sake of comfort and, when he would lean back in it, it blocked most of his view so he was able to drift off to sleep.
Good luck...I hope this helps!