Originally I left them in, as we were filling up with water we took one out, it didn't seem to make much of a difference.
The difference between yesterday's sail and what I normally do is the addition of another person. That weights brought us lower in the water allowing water to come over the boat easier, plus lowering the seats that much more below the water line.
I started another thread to get different opinions on solutions. Right now it seems a third party seat OR raising the hobie seat are the two main solutions.