If an area of the boat is going to be inaccessible, either 'hard to get a human in there' or 'not possible to access', then ALL components that build that area must be glassed ahead of time and you must seal all exposed end grain. Example: When you have the top of some chamber (a deck for example) ready to install, first make sure that everything inside the to-be-enclosed chamber is glassed, end grain filled and coated to seal, etc so that everything is waterproof. On the 'enclosing lid piece', also seal all edge grain and make sure that the piece is completely encapsulated and water proof. NOW you can install it, and if you can't reach in to apply fillets, then you have too put beads of thickened epoxy on nailers/supports etc (or on top edge of web stringers) and press the 'enclosing piece (deck or whatever)' into place and let it cure. Some things are impossible to fillet after the fact. That's OK. Just take steps to ensure that all parts are fully waterproof and encapsulated before final assembly.
Brian