cdl2, if you like carpet the best thing to do (in my opinion) is install one of the laminate or vinyl floors and then use carpet runners. When the carpet runners get dirty and worn out you throw them away and get new ones.
On the captains chairs, you'll have to either cut the flooring around them, or remove them, install the floor, and then bolt the chair back down through the floor. I'm no expert on this so before you take my advice on unbolting them from the floor, consult an expert and make sure it's okay to do that.