In my EuroReef skimmer manual it says:
"COOL TIP: If you do use such compounds ( above) , which in all likelihood most of you do, we strongly recommend that the pump be cleaned out quarterly by submerging and running it in a bath of distilled vinegar and water (1 part vinegar to 3 parts water). Simply allow the pump to run in a bucket with this solution while sucking in air for 10 to 12 hours ( overnight usually works great). After it is cleaned, remove the pump from the solution, disassemble, rinse, and scrub it thoroughly with freshwater so as to remove all visible debris (try our brush cleaning kit, part # ERBK-1). Reassemble and put it back to work!!"
this is the way I do it and it seems to work well.
Mike