I assume these are the charterhouse aquatics ones? They are pretty expensive, I don't think the benefit in these is worth the cost, I would maybe return them.
The bottom inlet removes debris from that level of the water column and gives nice even flow on that side of the tank so I would advise keeping both. I do have an aftermarket raised inlet on mine with a sponge as my substrate covers it otherwise. I don't cover the top inlet either so it acts as a skimmer.
I have my heater in the first chamber with a medium and fine sponge over the entrance to the second chamber. Sponges are easily removed for cleaning each week. The second chamber has two bags of filter media which are sat on a piece of rough sponge (replaced with carbon sponge if and when needed) to stop them going all the way to the bottom and again easily removed for a rinse once in a while. Final chamber has the pump which is also sat on a pad of rough sponge to help stop vibrations. I swapped the original pump with an eheim which is slightly more powerful and a lot quieter.
I've had good success with this setup so far. Flow is good, water is clear and stable and maintenance is easy. Are you planning to stock particularly messy fish? I have neons and a male guppy in mine (to stop him knocking up all the girls in my community constantly!)
I can get some pictures later if you like.