Give us some indication of how quickly the nitrate levels are raising, for instance on the fourth day after a water change, what are they?
Remember the more water you've got, the slower the nitrate levels will rise. Maybe you should consider getting a bigger tank at some stage?
As for the canister filter, I would fill all trays with biological filtration, leave a little bit of space for some mechanical filtration, maybe one or 2 inch thick sponge. Even though mechanical filtration is a good idea, especially with messy fish, biological filtration is what will cleanse your water of toxins. For this reason, get as much biological filtration into the filter is possible. Remember you can always gravel vac to remove the waste that has left behind.