I also have the JL600/6 and am using the stock speaker wires without issue.
When you swap out the door speakers, the cap will come out with them - so no problems there. If the cross-over is small enough, you can mount it in the door with some adhesive-backed velcro (available at Lowe's or Home Depot). This means almost no cutting of factory wiring at all. (Run the factory door speaker lead to the X-over, then run individual (new) wiring to the 4" and tweeter).