Well, I'd just leave it on the 3min prime Do you know why the system is losing prime when the pump is off? Ideally it wouldn't, and it means you have a leak somewhere (may or may not be significant). Do you have a bunch of air in the pump basket?
As for the skimming speeds, that just depends on trial an error, since each pool is different (amount/type of debris, etc). I'd probably start by running it as low as the SWG will let you, and then bumping it up if the pool is getting too dirty.