On the covers with 2 nipples one nipple was for the primer and one was for the recirc system. If you have the primer lines going in the top of the carb then you can cap off either nipple. If your recirc lines don't go to the by-pass covers then you can cap off both nipples. When we cap off both we just run a short hose from one nipple to the other on each cover.
I have a 1996 88SPL. Following pics show the bypass covers, nipples are circled in red. Both of them are part of the recirc system connected to the intake.