It is most likely water in the bilge is coming through the deck somewhere. Also, in heavy rain the lazeret hatch will allow overflow from the cockpit seats into the bilge, more likely while on the trailer or if listing port. I installed a 500 gpm pump in the bilge just aft of the bulkhead, in the lazeret, discharging via a thru-hull. I recently overhauled my boat and filled the thru-hull and when/if reinstalling the bilge pump will discharge into the cockpit by the cockpit drain.
Thru-hulls are the #1 cause of a boat sinking. If you install a bilge pump be certain to "gooseneck" the discharge hose to prevent backflow.
I've employed the method Louis recommends and it works well enough. On the other hand, while overhauling my boat and removing bulkheads fore and aft of the sole, found 1" holes drilled in the sole insert apparently intended for drainage, but glassed over during manufacture (therefore holding water in, causing the rot that necessitated replacing the bulkhead). During reassembly I drilled these through the new bulkheads so that if I were to pour a gallon of water into the v-berth bilge it would flow under the sole and to the lazeret bilge. Go to my profile and in an album there you will find a picture of the forward bulkhead removed, exposing the forward edge of the sole, and the hole I found. You will also see some of the work I did to take care of this problem on my boat (and common to many others). I hope that any water I find in the future can be dealt with using a rag. I'll be launching soon and will report how this all worked out.