The airbox sides fit over the cleats/chine logs on the bow and stern transoms, and so much be notched.

The hull (exterior) sides are just marked so you'll know where to trim the cleats/chine logs.

The chine log has to follow a curve. To help prevent the chine log from cracking under stress, I always start at the bow end, then use screws ever 3 or 4 inches.

Once the glue has cured, clamp all the sides together and plane or sand the edges so they match.