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Skimmers and canister filters basically have different functions. A canister filter removes solids from the water column, and a skimmer removes dissolved organics out of the water so that they can be removed.
I had a canister filter that I mainly used to run different media in, like carbon. The only time I put a filter in was during water changes when I would stir up any detritus so it could be removed. You can leave the filter in, just make sure you keep it clean, or anything caught in it will deteriorate, and can end up contributing to extra nutrients.
Skimmers are a pretty sound piece of equipment, but it is a personal choice, and is more or less needed depending on what you want to keep in the tank.