If you buy a good capacitor that will be a good choice and you will not have to deal with another battery. If you still want to do that just hook up the factory battery with the battery in the trunk and then hook up your system with the battery in the trunk, but there is a special battery you will need to use for better performance. Here is a site you can see a battery of this kind.
http://cgi.ebay.com/NEW-PYLE-BATTERY-STYLE-50-FARAD-CAPACITOR-CAP-2008_W0QQitemZ220300163297QQcmdZViewItem?hash=item220300163297&_trksid=p3286.c0.m14&_trkparms=72%3A1240%7C66%3A2%7C65%3A12%7C39%3A1%7C240%3A1318