For the first time, loosen the nut on the neck, tune it with the tuners on the headstock as you normally would. Then tighten the nut on the neck and dial it in with the tuners on the bridge. If you stretch the strings out good and get it in tune before you tighten the nut, you shouldn't have to mess with the tuners on the headstock again until you change strings.

Another tip if you use drop D: I back my bridge tuner on the low E way out (not all the way, you want some play both ways) then tune it to D on the headstock and tune it up to E on the bridge. That gives you enough play in the bridge tuner so you don't have to loosen the nut to move between E and D.