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You can fill through a baffled hole. I just put down two quarts through one side, then went over to the other side and dumped two quarts, and no problems.
I like the 2 holes. One for the pvc and one for the breather. I don't like the push in breathers and prefer a line from the air cleaner. It keeps the motor cleaner, push in breathers can become messy with oil fumes.
I understand now, I thought you meant 3 holes per cover. Yes, either 2 or 3 will work. You can fill and vent through 1 and PCV in the other or have 1 for fill, 1 vent, and 1 PCV. Norval is correct that the unit vent/fill caps do tend to ooze a bit and make your engine dirty.