As you mentioned, this priming pain must be very dependent on the model used. Do you have to do this every time you clean the filter?
I can't really share much, since my only experience with canisters is with XP's, but once you have them primed, you never have to prime them again, unless you disconnect the hoses themselves from the unit for some reason.
With those models, it doesn't really matter if you fill them up or not. As soon as you close the quick disconnect, water flows into the canister through the inlet, air goes out the outlet. I fill mine up, because I don't want the scare the fish too much with the sudden bubble bath from the spray bar (which is located on the bottom!)