It's somewhat complicated as I simply added a bus to my OEM fuse box and tapped into the power for all of the new items there. I also tapped into the OEM fuel power supply and ignition power supply from the fuse box. Essentially, I've still got the fuse box but with i think two or three added fuses. I can't remember right now. I've grafted both harness's into one. I've removed a bunch of grounds from the harness. If needed I can always add to them.
As far as keeping items from the OEM harness....I kept the starter signal, oil pressure switch, a/c, coolant temp, alternator wires. I also have to make a "y" harness for the speed sensor as it needs to go to the new ecu to deal with shifting the trans and it needs to go to old ecu for gauges. Theres more I'm sure, but my brain is fryed right now in dealing with al of these wires!!!!!