A.,
I am shocked that your doctor would recommend medicating your children to fly! My children are ten months apart and I have travelled with both of them from as early as six months. We have gone as far as Spain, from Las Vegas, finding that the children handled the flights better than the adults.
I have followed 2 general principals. 1. I am smart about booking the travel. Late night flights are usually pretty good for coast to coast flights or Vegas to Hawaii. If the flight was particularly long or with a long layover (which I generally try to avoid) then I get a hotel room. For instance, we had a 6 hour layover between NY and Barcelona. I booked a hotel room near the airport with the shuttle. Everyone appreciated the downtime, including the babies.
2. I always travel with a "bag of tricks." These are toys, books, activities that my girls have never seen before. Even as infants they loved the new items. I also make sure I am stocked up on Mylecon, Orajel or whatever was appropriate for their age maladies such as teething, etc. I also tried to delay their bottles to keep them a little hungry for lift off and landings as the sucking helps with ear pressure.
On another note, while I always relished the idea that kids under 2 fly free, I have since found that the extra seat is a blessing for spreading out, laying a baby down, etc,'
I think its great that your kids are starting flying so early. It makes is a lot easier in the long run. Happy flying.