Start with the speakers and work backward.
Decide how many speakers you need. How many subs you need.
Then get the amps you need to drive the speakers.
Decide what kind of source you need (i.e. AM/FM, CD, XM, iPod, etc.) and get a head unit that will handle those inputs.
Then get enough batteries to drive the entire system. You may need to upgrade your alterator also.
Use high quailty wires thrughout. Don't forget about the remote(s).