I assume you're talking about carmelizing the first runnings? Usually that's what's done- carmelize the wort before adding the hops. Boil the wort down, and then proceed.
If you're doing it the way I think, you still top up with the same amount of water in the fermenter for a 5 gallon batch as you normally would- that is, up to 5 gallons. You should have a 5 gallon mark on your fermenter, and should top up to that level.
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