Talk to the colonel and he'll ask you to head over to the helicopter crash site and recover the weapons there to beef up the defenses. Once you found the chopper, place your boat to the nearest shore then carry the machine guns there. You can throw the MG's off the cliff to make your job easier.
Once you're back in the mission building, set up the MG's on any of the four positions. It will be a good idea to place one MG in front and the rear of the building. The mission will be complete afterward.