On the Water
Tempering - Often the river/lake water is colder than the air you fill up the raft with. So after you inflate the raft onshore, place the boat in the water for several minutes (make sure you secure it well). The cold water will cool off the air inside a little bit causing the air to shrink. At this point, use the mouth valve to "top it off". In extreme conditions, i.e. glacial runoff water, you may need to repeat the process a few times by stopping every so often until the raft is inflated just right for the conditions. Also, if the sun is out and your boat is sitting on the beach for a while, it's a good idea to let a little air out of both the boat and the seat. When the air in the raft heats up it expands, stressing the raft unnecessarily and potentially causing damage.
Don't Lose Your Gear - From our own experience of almost losing several rafts to the great white Pacific, always tie up your rafts or secure them in some way. Pulling them up on to shore out of the water might not be enough, the wind always seems to pick up as soon as you doze off next to your lunch campfire. Hold on tight to those paddles too. You don't want to get stuck up the creek without a paddle! Hah, hah...sorry. Anyway, just remember, your gear is your trek.
Cargo - For some great pointers on how to strap your pack, skis, bike, etc. to the raft, check out this link from Alpacka.