Installing a 6000btu system on a 30 foot boat would not accomplish much. Probably better to install a portable unit in forward hatch for use while you are aboard. Personally, if I was incurring the expense of a built in system I would install a 12,000BTU self contained reverse cycle AC/heater. I have no idea of the layout of your boat; however, you may consider developing a layout & forwarding to Flagship marine air-conditioning systems in Florida. Flagship builds custom systems to fit your dimensions/requirements.
@kloudie1's suggestion for a split series system is a good one. The PO of my boat installed a cruisair-dometic emerald series 16000btu split system. Don't know how much it cost, but probably $$$. Very effective in cooling the boat during our brutal summers. Hate to think about future costs if the two air handlers (evaporators) become a problem because the entire system will have to be evacuated, component replaced, re-evacuated, & recharged. If possible, I would much rather a self contained unit; initial cost is less, simpler design with less components, less susceptible to leaks, & less expensive to repair/replace in future. Good luck!