Ditch the polyfilter material, while I've found that it's good stuff for a brief period, it clogs up too fast to be used in a canister filter (I'm speaking from my own experiences here, my flow was greatly reduced within 3 days), and replace it with a filter sponge. I dont know what shape your canister is, but you can probably get a filter sponge from your LFS that will fit it, or that you can cut to fit. You will continue to use this filter sponge almost indefinately. Everytime you clean out your canister, you'll just wring the sponge out in the water that you pulled out of the tank into a bucket to keep the pre sponge clean of large debris and waste. The polyfilter material while it can be rinsed out, it will clog up all that much quicker, because theres a lot of waste in the polyfilter material that you can't really see, it may rinse to white again, but it's still going to clog up all that much quicker.
So, bottom tray being No. 1 tray, top tray being No. 4
No. 1 Prefilter sponge < to keep the larger particulate matter out of the rest of the filter.
No. 2 Ceramic rings
No. 3 Substrate pro, or get more ceramic rings
No. 4 Hold empty until you want or need to run things like carbon, or other chemical filtration.
You can of course do as you please, but I've found the polywool filter material while good at collecting the really miniscule particles in the water, isnt worth the trade off of having to replace it and or rinse it every 2 or so days. I suppose if you dont mind the reduced flow rate, you could run polyfilter in the No. 4 container to do a fine polishing, but its still going to clog up pretty quickly.
My cascade 1000 came with the polywool material and lasted about 3 weeks before I realized that, the polywool was what was reducing my flowrate in the tank.
Now I've got a prefilter sponge, and 3 empty containers (because this canister has been transfered over to a saltwater tank, and I dont want any ceramic rings or bioballs to up my nitrates), that are used usually when I want to run carbon.