We flew from RI to CA last summer with our two kids; my son was 14 months at the time (and 4 year old daughter). We brought his car seat and it seemed to keep him quite calm. We hadn't used one on a plane with our daughter when she was younger, and I was skeptical about how it would work out, but he seemed fairly content throughout. He definitely had a few squirmy moments, but overall I was pleased, and will bring it again when we fly the same route again this summer. People had said that because kids are used to sitting in them in the car, they accept it on the plane. That was my experience.
As for the cold, bring along things he can suck on to help clear his ears (same for your daughter). Sippy cups of water and/or a pacifier if he uses one. When my daughter used a pacifier, I allowed her to keep it during the whole flight (at home it was only for sleeping, so it was a treat). We did have one flight with her when she was sick and it was hard. I wonder if there are any natural decongestants that he could take? I never looked into that.
The other part of staying content is to bring lots of toys and snacks. Just keep rotating through them. Finger plays and songs to entertain are great, too.
I hope it goes well. I would love to hear an "after" report and anything new you learn along the way - we travel regularly.
K.
SAHM to 5 year old daughter and 23 month old son.