The image below showed how my boat builder lead the lines through the bulkhead beneath the fixed windshield. While this might let more water through (compared with Dan's arrangement) in event of "green water" coming over the deck, it does keep things dry enough in normal heavy rain and spray so a cell phone can be left behind it.

Note they used separate pieces to form the bulkhead, and joined them with 5200 or equivalent. This approach would allow a more serviceable arrangement for the retrofitter: You could cut out a section of bulkhead to make your path for lines, making the cuts slightly slanted so the removed piece is wider at the top (like you'd cut the lid of a pumpkin). Then remove enough of the the lower portion of the piece to let your lines pass, do fiberglass/gelcoat work to refinish the deck and sides of the cut beneath the removed piece, and put the upper portion back in place with 5200 or equivalent.

Note: When doing the fiberglass work on the "floor" of the line passageway, make sure you slope it about 5-degrees so rain water and spray will normally drain out forward rather than aft.