I am wondering if the "two holes" you are talking about are one of the two things:
1. Holes for the rail attachment at the rear commonly used to attach tubes and or/Magma type grills. CougarCruiser has one on his 318 Vista
2. The holes that "vent" the swim platform...about 5-6" diameter. These allow the boat to bounce and relieve water/air instead of putting stress on the swim platform. They also let it drain easily when you come off of plane and your wake catches up with the boat.
Are yours the two seen in this pic:
