Did you look under the bottom to see if they punch out? Some do, some don't. If not an end mill will no doubt do the neatest job if you have the means. If not a good drill bit will work fine. PCV grommets and filler/breathers come in a few different sizes. Your best bet is to look on Summit or JEGS and find what you like and drill the hole sizes they call for.
PCV on pass side and fill on drivers side is the way I always do it but it's not written in stone you have to do it that way. Just have to have one on one side and one on the other
Oh yeah, make sure to install baffles if they don't have them. Without baffles the PCV valve can suck up oil splashed on it and the breather may spit out oil splashed on it.
