I run a Rule 2000 in the stern and a Rule 1500 in the bow... Both are wired for Manual/Automatic, I've never had to turn the 1500 on, but she's wired for automatic just in case.
As to your wire question, both 4 and 2 are overkill, but if you're fixed on using those sizes then my gut would say go with the 4 over the 2 simply for it's flexibility. Max amp capacity in normal 115v conditions is 135 amps for the 4 gage, and 181 amps for the 2 gage. But amperage ratings are very different for common/typical 12V DC automotive usage. For example, a 12 gauge wire is commonly rated at 20A for 110V AC home usage, but in automotive 12V DC usage 12 gauge wire is commonly used for circuits carrying 60A. It would really surprise me if you reached anywhere's near 100 amps total in your boat with everything running full bore.
But if you want to be 100% certain, look up the specs on everything you are running, find out what each one's amp draw is, total them up, and you will then know what wire size you actually need.... I'd be willing to bet that 8 to 10 will work fine. (and fyi, I ran 8 in my boat from the battery to my fuse panel, then 16 [20A] gage from there out to all my do-dads.. lights, horn, instruments, etc.) Hope this helps.
__________________
1987 V20 w/1987 150HP Yamaha on a Shoreland'r Trailer
1978 16.5 Airslot w/1996 120HP Force on a Four Winns trailer
1996 V21 w/1993 200HP Mercury on a Shoreline Trailer
All towed by a 5.7L Hemi Durango.
If God didn't have a purpose for us we wouldn't be here, so
Live simply, Love generously, Care deeply, Speak kindly.
(Leave the rest to God)
Silence, in the face of evil, is itself evil. Not to speak is to speak, not to act is to act. God will not hold us guiltless.