I generally make a new wanted list for each set I'm trying to complete - that way I can see how many pieces I need and what they are. If it's a set I'm going to sell, I search my wanted list by just those sets, thus giving them "priority." Once I narrow down a few shops by unique lots, I compare prices. Then once I pick a shop, I make sure to search the shop for my entire wanted list to be sure to pick up any other pieces I may need.
It takes a little tinkering, but works ok. Don't forget to then delete items ordered from your wanted list or else you end up ordering again!!