Wait, are you using a stock head unit? If so, you don't need to thread anything or do anything in the cabin, ITS ALL IN THE TRUNK ALREADY.
If you are using an aftermarket head unit I would just run a 6 channel RCA down the center of the car on a coupe and across the drivers side and down the footwell to the hatch area through the grommet behind the driver under the carpet.
However, you don't need to do anything if you have a stock head unit.
Just look at this diagram and splice the leads accordingly into the amp and then wire the speakers into the crossovers. That's all there is to it.
2001 Alpine / Schwartz Coupe
2001 Estoril / Estoril Coupe
2001 Steel Grey / Estoril Coupe
1999 Estoril / Estoril Coupe
Sunroofs are for girls.