If your going to use a canister filter, you will need to clean it often, usually every week or so. I would use it with a filter pad for mechanical filtration. The only other media types I'd put in it would be carbon or GFO and similar media. If you have any bio-media, you can remove it. The biological filtration in a reef system is from all that live rock you put in the tank.
Assuming that your not planning on a sump, I highly recommend that you invest in a good hang on the tank skimmer. Something like an AquaC Remora should work just fine. Avoid the bargain skimmers. There area a lot of junk ones out there.