Generally, unless a school asks you to list recommenders (many do), you will go complete as soon as they receive the minimum number of recs. If you do not add a school to your list of schools where you are directing specific LOR's (this is easy to do) then your general LOR's (up to the number accepted by the school) will go with your report, and you will end up complete and possibly have your application reviewed before your best recs get there.
I think there are a few different ways to proceed, based on the specific applications we're talking about:
1. Schools that will let you go complete now but apparently don't start review until later (a combination of LSN and people here might help you get an idea of this): For these, you can sometimes afford to go complete earlier than when your best recs are available (still getting the early-completion advantage) because they will add new items received before review to your file.
2. Schools that will let you list recommenders: These will sometimes give you the option (or, by default) to hold completion until the specific recs you want are available. That said, you probably lose the early-bird advantage.
3. Schools that will let you go complete as soon as they receive the required number of recs, and will review your file soon: at these schools, you can help keep yourself from going complete by adding them to your list of schools for specific LOR direction, and waiting until the other two recs come in to specify that these should go to the schools. Of courses, you probably also lose early app advantage here. Keep in mind, though, that if your app is held for later consideration or if you are waitlisted, you can always have the other recs sent later.