Like mike said there is nothing wrong with running your canister filter. If it has sponges in it just make sure you clean those often. They collect a lot of nasty stuff out of the water and can end up breaking a lot of that down and putting all of that back into the tank as excess nutrients. If you do weekly water changes i would make it a habbit to clean the sponges when ever you do your water change.
If it were me i would wait on the HOB
skimmer. You can make up for it by just keeping up on your water changes until you are ready to plumb in a sump and get an in sump skimmer. I've heard of skimmers getting cloged our out of adjustment and pouring a lot of water on people's floor. I also think most of the good quality skimmers are in sump.