I find I have greater success if I bottom super, rather than top super. Esp. with foundation. Bees start working the foundation quicker. They'll finish off the top super, but don't like that great void between them and the top super they've stored honey in.
Some folks think a full super on the bottom acts as a "cap" indicating to the bees they're full, when they're not if empty supers are on top. Granted, I used to top super, as it was easier. Is either way right or wrong? nope, just is... do what you want, and see what works best for you.
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