Within the canister filter, there are usually a few media baskets and filtration media depending on the make and model. They do come with your initial purchase of the canister but its up to you if you want to use them.
There is usually one for biological filtration which means this stuff in the basket would encourage the growth of beneficial bacteria which would convert ammonia to nitrite and then to nitrate. Another layer would be for mechanical filtration which means it remove solid waste particles from your system.
The canister unit usually gets too efficient and then your system gets loaded with nitrate though not as toxic as nitrite but it is still bad for the growth of corals, invertebrates and fishes alike.
If you really need to use one, I recommend that you not use the media in the lower basket...just place a piece of fine wool material for mechanical filtration (to remove debris and suspended solids)
Secondly, fill the upper media basket with a media called ' biohome' which is made of sintered glass material which is known to encourage both the growth of aerobic and aneaerobic bacteria which would remove nitrite as well as nitrate from your system.
Finally, if you want to further improve your filtration system, you could add chemical filtration to your system by adding activated carbon...Here I would reccomend the 'Chemi pure' media.
As all reefer knows it, it still pretty hard to tell at this point of time if your system will be susceptible to high nitrate reading after all the above measures but if you still face problems, perform a partial water change (20%) on a weekly basis and major 50% water change on a monthly basis.
Hope that helps.