To answer your question directly, you would want to seal the engine so that you can pull a vacuum in the crankcase. This would include turning your main seals around backwards because they will now function in reverse. Depending on how much vacuum you are able to pull, you may need a regulator so you don't pull too much and suck in your gaskets. Your pump may have an integrated regulator.
Now, to address some real issues. First thing I would suggest is doing a leakdown test. If you are leaking more than 15%, you are blowing a lot of horsepower right out of that dipstick. Ring seal should be a top priority.
If your leakdown is within acceptable parameters, I would then evaluate if you have sufficient crankase ventilation. You really need more than just a PCV setup on a boat. Do you have open breathers? Are they of sufficient size? If you have an option, I would make every effort to mount them towards the front of the valve covers, with proper baffles.
I really wish people would stop recommending vacuum pumps for blow-by.