This what I did to mine, left seat in but built a platform. On the newer Fords they put in lockable storage under the rear seats but the only problem is when you want to put something in the rear and not have it ride on the seat you have an uneven floor area. So I built a platform that covers this storage area and made the lift up lids lockable so I can still lock the lids down (I know it won't keep anybody out if they want in) and helps keep the platform in place. My wife also made some covers for the back of the seats and console to protect them from getting scared up. Then we got a dog seat cover and used it to protect the rear seat that is folded up.
This shows the lid in the open position with some tools in the storage compartment. The lid is a 2 piece so one side can be opened at a time.
This is on the drivers side with a storage box, I have another one just like it and they stack. Then I installed some tie downs to strap them down to keep them from moving.
This is the passenger side with a 2" foam pad for the dog to lie on.
This is the drivers side view