the squares are little metal restrictor inserts. your intake has the crossover tube in it. if you use a gasket with it blocked off, eventually the water will penetrate it. the crossover tube is to warm the intake air when cold to help with keeping a constant air intake temp for smog and smooth idle when cold in a car, and also to cool the intake from the hot oil splashing on the intake manifold from the cam whirling around. honestly with the oval port heads and intake you're not exactly going to notice the difference with it open or not. MOST aftermarket intake manifolds are gonna have it blocked off.
Not to be picky but water does not flow through the crossover. Exhaust gasses flow through there. Yes it heats the carb base to help cold start, but mostly it's an EGR port for emissions, which boats don't have, so yes it should be blocked off.
OP, the cardboard intake gaskets will work fine. Make sure your surfaces are clean, and put a very light coat of silicone around your water ports on each end. Throw away the end gaskets and run a bead of silicone on each end. Let your silicone sit to "air" about 5 minutes before you set your intake on it. Tighten from the center out and don't over tighten the bolts. Torque is 25 ftlbs . I've added a link from Edelbrock that shows the sequence at the bottom. Good luck.