Stereo and Amp set up question

OK this is what we are working with:

Head Unit: Sony CDX-M50ip - 4 ch pre-amp outs (Front R&L, Rear/Sub R&L)

Boat Speakers: Kicker KM6200, JL Audio sub (I don't recall what model)

Amp Powering Boat Speakers: Alpine PDX5 - RCA inputs: Front R&L, Rear R&L, Sub R&L

Tower Speakers: Kicker KTM6s

Amp Powering Tower Speakers: Kicker ZX450.2 - RCA inputs (R&L), RCA outputs (R&L)

My question is how should my RCAs be run?

All of the equipment is installed and working but after experiencing some noise issues we looked at the wiring and discovered that the speaker wires were connected wrong (- into + side) so I suspect that there is also an issue with the RCAs

THANKS FOR YOUR HELP!!!