The bottom part gets the cleanest water. Please read here:
http://www.hagen.com/pdf/aquatic/FX5_user_manual_EN.pdf
It would be on page EN-13: upper for pre-filter, middle for chemical, bottom for BioMax.
The pump is indeed on the bottom but I think that the water gets pumped up 'from' the bottom through a tube running alongside of the canister, and the dirty water gets in from the lid, passing through the baskets.
BioMax (Middle or Bottom Media Baskets)
A-1456 (500g)
A-1457 (1100g)
Carbon (Top or Middle Media Baskets)
A-1440 (3-pk., 100g ea.)
A-1445 (375g)
A-1447 (900g)
A-1448 (1650g)
Polishing Pad (Top or Middle Media Baskets)
A-246 Water Polishing Pad
A-248 Fine Filter Pad
Pre-Filter (Top or Middle Media Baskets)
A-1470 (750g)
For freshwater and marine environments