Some pictures would help if you have a way to provide them, or let us know what the manufacturer of the tank is and we can look it up for you. I would be skeptical about using a foam pad for substrate. That seems like it would be too much work to change out when needed. It may have been some sort of shipping protection but again, its hard to tell without a pic. IMO ditch the foam and use a traditional gravel, sand, or shell substrate.
The external filter sounds like a wet/dry sump setup. If you can get a pic I can explain more, if not try to describe it a bit to give us a better idea of what you have.
Browse through the pictures in this thread and tell me if anything looks similar to your setup:
Click this Link.
Pic would sure help 
