I have the same problem after some good weekends, the boat starts to stink really bad. I never really wanted to get my pressure washer in my boat like a lot of people recommend, so the next best method I found is to use a water hose, vacuum(I use an old carpet cleaner) to suck water and a scrub brush.
I wet all the carpet down with the hose and use the scrub brush and some kind of cleaner to scrub the carpet. I then suck up all the water and repeated this cycle until I get tired. I've done it for hours and have yet to get the water I suck out of the carpet to be totally clean. I even use some fabric softener in a couple of the last cycles to try and get the carpet smelling good.