ok it will help immensly with pictures ok,
let me see if im getting this straight... you could use RCA cables if the head unit supports it so RCA to amp then to speakers...
but yeah pictures would help sorry... in mine i have:
2x 10cm speakers at the front from headunit wiring
2x 6x9's on the parcel shelf from headunit wiring
1x Amped Sub from the RCA outputs