Hi, welcome to ribnet!
From the sounds of things you've actually got a SIB. The way to get the floor boards in is to totally deflate it, insert them (the toobs will roll out the way) then re- inflate, being a bit careful as the toobs take their shape to make sure the baords are in the right place. They then get trapped in the corner of the floor & the toobs and give the boat a bit more rigidity.
The hole in the front one is possibly to give access to a keel inflation valve or some davit type fitting for the back of a big yacht?
Out of curiosity, is the outboard 2 or 4 stroke?
Any pics? That might help us to figure it out.