just use the stock wires that are there and then connect the stock wires to a new set of wires that you will then run to your amp....
To make that more clear hook your speakers up using the stock wires that are already through the door. Then you connect the stock wires to another set of wires where the wires end up by the head unit, then run to your amp. It makes it alot easier if you so it this way...
Let me know if this is still unclear