Look for more grommets
A tip for automatic cars: if there is an MTX version of the car available, usually there is a grommet where the clutch pedal would have pushed thru to the tranny. This is the case in the 6th gen accord: I popped out that grommet, cut an X in the middle, and it fit a 4 ga power cable perfectly.
In my Dodge Neon, I just used the main wiring harness grommet........its a good spot, because its made in such a way that the entrance to the grommet is recessed from flush, so water cant get in..........poke a small hole in it and feed the cable thru.
I drilled a hole once.........I will never do it again. It wasnt hard to keep it sealed, but Id rather just spend 30 extra minutes trying to plan out where the wire should go without drilling. You'll be better off the in the long run.
And yes, keep the RCAs separate.........I usually run the power down the side of the car where the battery is, and the RCAs down the opposite side (although in the Accord I ran the RCAs down the center console, it was easier than risking setting off the side airbags).
I guess the biggest thing is you just need to take your time and plan things out before you start installing.
Good luck!!!!
-Chris