I agree with previous posters.
You have a set of covers for a carbureted engine, and you will make things hard on yourself and your engine by trying to use them on EFI.
Sell them and buy a set of covers for EFI use.
You said yourself that you are going to have trouble filling the oil.
The hose to the intake plumbing from the cover is there to allow the PCV valve to evacuate pressure/fumes from the engine case without taking in unmetered air and acting like a vacuum leak. You can add this feature to your carb'd covers, but make sure to add enough space below the port, and/or baffles, so that it does not suck too much oil into your intake.