first, using the design plans for the rooms you want to wire, consider how you will layout your furniture and where the speakers will go (5.1 or 7.1)
then determine what type of speakers you want to use - - stand along in-room speakers (towers and/or bookshelves) - - - in-wall speakers - - - in-ceiling speakers (but please, only for surrounds - not the front 3)
determine where your TV and the supporting electronics (sat or cable box, a/v receiver, network attached a/v devices) will go. This is a great time to have your electrician put a dedicated 20 amp circuit with quad receptacle outlets in for each room at the equipment location. If necessary, the TV can easily be on another shared circuit.
buy some 12 gauge, or 14 gauge if you need to save a few bucks, speaker wire rated for in-wall use (rated CL2 or CL3) by the National Electric Code so the inspector (and electrician) won't give you any grief.
this is also a good time to run CAT5e ethernet cable to the rooms with entertainment systems and some other rooms where computer equipment might live. If a multi-story house, definately run several CAT5e to each level. Home run the CAT5e to the location where you and your electrician think the cable TV-internet or phone line DSL will enter the house. All the CAT5e will connect to the internet through a router or ethernet switch.