Stereo wiring-running wire
 

My question is as to whats ok to run next to each other. I know I have heard its not OK to run certain stereo wiring next to each other because it can cause speaker noise. Question is as to 4 gauge power wire from the battery to the amp and then 12 gauge speaker wire from the amp to the speakers.

Problem is I only have one place to run them from the stereo/ amp location to where the speakers are on the elevated fly bridge. I'm kinda stuck running where the current factory stuff is. I can separate it part of the way but for the final 4-6 feet there's really no way to separate. RCA's I can keep away, but not the speaker/ power wire. Is this going to be an issue?

pretty good chance you'll hear some sort of noise with it run like that... or possibly nothing at all. power should be kept away from rca and speaker whenever possible though.

You will probably be fine. The high impedance "RCA's" are much more susceptible to picking up noise than the low impedance speakers.

Is it going to help if I wrap them both in separate plastic loom where they have to run together?