The car seat is a good idea although we never tried it.
Make sure they are not strapped in because they would certainly drown in a flip before you could free them from the seat.
We always held our kids when they were infants or laid them down on the deck when sleeping. Mine is 24"x42" with foam camping pad glued to it for comfort. Now they sit on the deck when not rowing or stand in the floor.
You have to watch them at all times since they are never prepared for a bump from a rock or shore and would topple right over in the water or hit their head on the frame or something.
The other thing I woul recomend is to make frequent stops for snacks, and play time so they don't get bored and cry all the time, which with an infant is highly possible seeing that life vest ride very high on their face and really piss them off.
An umbrella is a nice addition also for desert floats.
Our kids are anow 5 and 2 and have been practically rafting since they were born. The hardest thing now is finding enough quiet time where they are not hounding me to let them on the oars.