For most of the wires you just pull them back through the grommet that goes through the firewall and re-route them inside the car. Some go to the SMJ and others to various parts of the car. I made a new fuse box and relay spot behind my glove box. Then the wires run to where they need to go from there. I had to lengthen some wires and shorten others. Its a tedious task but to me is well worth the work.
Check my build thread, there is some info in there on what i did with the harnesses.