I have a Tiderunner and it has a similar system. I don't have scupper valves and I use drain plugs to cap the inside of the scupper. When I start to accumulate water, from rain or whatever, I pull the plugs and either get it on step, or put passenger weight in the right spot to drain the sides one at a time. The good thing about my boat is that the deck hatches rest on top of channels that don't allow the water to get into the bilge normally, that is unlees you really get a lot of water going. I have never taken any quantity of water into the boat, so it hasn't been an issue.
Beeeeeeeeeee