well if you had the pipe at the top, how deep would you have it? the reason i ask is because if your water level dips below that even temporary, the canister will run dry, and/or have air sucked into the impellar housing, and result in more work for you.
i have an old fluval 303, that i dread having to clean every month because reguardless of how careful i am, air enters the system and breaks the syphon, or excessive amounts of air bleed into the canister body, and eventually get into the impellar housing causing me to tip and shake the unit a bunch of times to get the canister functioning again.
surface skimming is always the best course of action, for any filter. simply because it can remove a film that sometimes collects at the surface that can impede the oxygen replentishment cycle (co2
being exhausted from the water, and having oxygen pulled into the water, to balance pressure) however if you have enough surface agitation it probably won't be needed. the only benefit to pulling water from the bottom of the tank, is that some solid waste might be taken up and keep the tank/gravel more visually clean.