I have posted a few budget systems here in the past, you should be able to find them if you search.
Basically you could do it for about a grand.
Any head unit, two four channel amps, four 6.5" coax speakers in the boat, a single 12" sub, EVID tower speakers. The Clarion APX480M amps are not a bad choice at your price point, ebay. Alpine Type R sub, ebay.
amp 1: two channels to the four boat speakers, two channels to the sub.
amp 2: four to two (2x mono) config to 8 ohm speakers.