Where does the predicted media go on the bottom or top and also the ammonia remover
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Pre-filter media is useless in the FX5 or FX6. The water passes through the sponges first. To put pre-filter media after sponges is not going to do anything beneficial.
I don't know why it works but, the way I have my setup though the prefilter does work in the top tray. I get just as much buildup in the entire top basket as the other two combined and quite often more.
The point of pre-filter media is to slow the water velocity and spread it out so that large particles fall out of suspension and don't clog finer media such as sponge and floss. In the FX5, after the water has passed through the foam it is cleaner than what would ultimately hit pre-filter media. Since the FX5/FX6 uses a downward flow through the trays the pre-filter media is increasingly useless since the particles can't settle out like in an upward flow system. In other words, the pre-filter media just passes the majority of particulate since it's constantly flushing itself out into the second tray.
I think that the reason you see buildup at all in the upper tray with prefilter is because the sponges of an FX5 have lots of bypass potential and limited holding capacity. Once the sponges are full of particulate they start to release into water and carry these solids into the following trays. I don't think the evidence of particulate in the trays is evidence of them effectively cleaning the water but rather of the system bypassing water.