ok here is what i did with my fluval 1 plus so it can handle the work load it's put up to.

there is a small offcut of micron filter just inside the intake holes and more block pieces to hold that into place... works well.
this is my whisper 30/60 with original media replaced because it became a bit ridiculous buying more media every month.

this tank also has a canister on it filled with some rocks in one tray then various size pads then polishing sheets then a micron pad last step is also a polishing pad for bacteria.
i had just done cleaning on the canister and the fluval will be waiting till sometime tomorrow if you'd like to see more.
remember the whisper (hob) is only there for a supplement and for easy fertilizing and feeding of fresh foods so it don't have a micron pad and the micron pads don't work so well on a hob as it will just spill over (the water) instead of flowing through. notice the piece of block in the middle that keeps the water from escaping through the front instead of going through the media.
in your setup i would place my pump in a block cut to fit where needed and make sure the block is taller than the water level. this will ensure the water has to flow through it. you can also use polishing pads/sheets that are a little looser as micron pads tend to restrict flow which could be an issue for you. just remember bigger holes first when pertaining to direction of water flow.