Yeah the floor sits almost directly on the top of the wheel well.
It's not a problem to drop the floor it you are doing a wheels up or non wheel (5) version.
For the 2 I'm working on to install the PE floor I added a strip of plastic under the flooring so the PE has something to sit on since it's held together with 4 tiny tabs.
I then marked off where it will be and cut areas around it and the front so the foot pedal area is over open space like on the real ones.
For the 5 that will be in flight mode I dropped the floor to accommodate both the open door at the rear and a figure in a seat.
In both cases I put the seat on a block of plastic so it's raised off the floor.
I also added the front bulkhead with opening and walkway.
The #2 bulkhead between the cockpit and radio room is missing the openings for the cables to run through on the outer edges.
Eric...