ok i thought of a better way to explain this... i had this same setup.
you need to cut the bypass harness (the one with 2 ends) apart. one of these ends matches the output connector from the factory amp that goes to the speakers. that is the one you want to use (so you can cut the other end of the harness off close to the connector). now you will need to make about a foot (? check this length) extensions to each of these wires. you splice these now into your head unit's output wires (harness or otherwise). the grey bundle of wires (it was grey on mine) that went between the stock HU and amp does not get used. you can take it out or just leave it there. none of the other harnesses or connectors that come in the bypass kit are used.
my SVT was really only my 2nd car stereo install and it wasnt difficult.
. Easier and will sound best.