It might help to say what kind of canister you have. There may be quirks to certain brands/models.
I've only worked with a couple of brands of canisters (Eheim and Hydor), but here's what I can suggest.
My canisters have all worked by siphoning water out of the aquarium, then pumping it back up to the tank. To maintain that siphon, I find it helps to place the filter well below the level of the tank (mine end up on the floor or in a cabinet underneath), make sure the intake is well under water so that it never sucks air, and that the hoses are as straight and short as possible (without extra loops or long horizontal - or uphill! - runs).
If you're not able to re-prime after emptying the filter for maintenance, that's a separate issue. My procedure there is to cut power to the filter, then close the in-line valves on both the intake and outflow sides. Disconnect the filter and do whatever maintenance is needed, then hook it back up. Then open the OUT valve (goes to your spray bar or outlet) first, give it a moment, then open the IN valve (goes to your intake). Usually, the siphon will then fill the filter, pushing the air out through the spray bar - it takes a few moments, but if your spray bar is under water you can see/hear it happening. Give it 30 seconds or so to equalize, then turn the filter back on. I almost always have a prime at that point, and everything kicks back into gear, pushing out any remaining air bubbles.
If I screw it up and have to re-prime the filter, what I usually do is take the hoses and dunk them in the tank with the valves open so that they fill with water, then close the valves and re-attach them, and try again. You can also try filling the filter absolutely full of water before re-attaching it.
