Use one set of holes for the PCV, the other for breathers.
Many years ago(I wasa 16 I think) I aquired a beautiful set of ribbed cast aluminum valve covers for a 318 I built for a 67 Charger. I spent a month polishing and detailing the valve covers and they looked great. The VCs did not have place for PCV and I didn't have breather caps, just tight fitting oil fill caps. On my first test drive on the new engine I made it about 5 miles when massive amounts of smoke started coming out from under the hood. Needless to say I about messed my pants. I checked under the hood and everything was covered in oil, the dipstick was about halfway out of its tube but I couldn't see anythign else wrong. I checked the oil, added a little and headed back for home only to have the same thing happen again.
Basically the crankcase pressure built up and the only place it could go was out the dipstick tube spraying oil all over everything. What a mess. I didn't want to drill the valve covers so I ended up getting a breather cap with provisions for a PCV valve which solved my problem. I miss that car

I guess some lessons must be learned the hard way

Bobbyt