Be prepared: A productive soundcheck can be done in well under an hour. Arrive early! If you spend too much time loading in, it can cut into your critical soundcheck time or even eliminate it altogether.
Get ready to hit the stage: You know your set, so set up your rig appropriately in advance. This includes the number of guitars needed (don't forget the spares), your amp and FX pedal settings, and preparing the proper cables and power supplies. Dial in your amps' settings beforehand; you can adjust them during soundcheck as needed. Same deal for your pedals--have them set and ready with new batteries.
Accept that the sound engineer knows best: This is the time when the engineer can help take your music from sounding good to great--if you let him. The engineer is in the best position to judge and if he asks you to turn down the volume (a common request) or change up your sound, he's got your back. Also, don't forget that the audience absorbs sound and rooms without people can sound boomy and bad.
Soundcheck isn't a rehearsal or performance: Soundcheck isn't the time to just plug in, let loose and start killing it on stage. Nor is it the time to toy with new songs you're writing or performing your whole set. This is serious preparation time that sets the stage for the quality of your show. play snippets of at least two songs. Choose your loudest and quietest tracks as they give the engineer more to work with, and play songs that use all your instruments and mics at once.