Well the answer to your question is pretty much there dude. You have a PLUMBED BACK BOV and now you've installed an ATMOSPHERIC BOV, which of the 2 do you want? One just recirculates the air back thru the system while your new vents it out. Either have one or the other. No damage can be done to the car having both, but it just defeats the purpose of having an atmo bov on there now.
Like what was said a few posts up, if you can't get your hands on a block off plate for your stock bov, get a coke can, use the gasket off the stock bov trace around the can and cut it. Use that as a block plate and whack your stock bov back over it.