Keep it as short as possible. Heat/fire is your #1 enemy in running a hot-wire to the trunk. Depending on your alternator and how much you are going to discharge your aux battery, you might need anywhere from 0 gauge to 8 gauge power-wire. Put in a fuse between the output of the isolator to the second battery, within 6" of the isolator, and you should be okay.
Hope this helps.