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Folks say just add bio media in all 3 baskets. But the Fluval manual says add different types of media including bio media in all 3 baskets.
 

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I personally have bio in 2 out of 3 trays. the bottom I put some filter floss to finally polish my water. other wise I would just use bio as it has mechanical filtration all around the outside of the baskets.
 

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I put in Purigen (just because) and prefilter in the top basket.
matrix in the bottom two

(there's a ton of posts about this, just search for fx5 media)
 

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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
 

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The manual is a guideline, not an absolute rule. I found (along with many others) the filter works best with the bio media in all 3 baskets. It says to run carbon, but it's been established that carbon is useless unless removing medications from the tank. I've also found that the polishing pads that Hagen makes clog very quickly (Much quicker than filter floss bought at walmart) and slow output of the water down quite a bit. You don't think Hagen wants you buy replacement pads and carbon? Like I said, the manual is a guideline in my opinion.
 

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Oh for sure I buy quilt batting and polyfil in sheets to cut to fit. I really don't run much media after it goes away just pads and foam.
 

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I have biomax in all 3 baskets with polyfill on top of the bottom basket.
 
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