I'd remove one of them, and keep the other.
You'll use bulk heads to plumb things from the holes in the bottle to the canisters or sump or a mix of both filter methods(best IMO).

One set of holes will pipe water from back to the top and the other will get the lower(to and from).

Overflow will be be for a sump, the bottom set will be for a closed loop cainster(say an Ehiem 2260 etc). Add a filter screen like a lifeguard type and a return with lok line.

Take a look on line for various sump diagrams.

Regards,
Tom Barr