How can I make a hole only affect a single part in a part studio?

Should be a simple answer but I'm having a bit of trouble here. Basically I have a small box shaped feature on a part with another part that is a sort of lid fastened with four screws. The lid needs clearance holes for the screw but the box part is going to have threads. I've used booleans and things before and there is a way to dictate what part is affected by the operation but I don't see this option for holes.

Thanks in advance!

https://cad.onshape.com/documents/1b3c67dbe3e1a91d3e53c5a5/w/6acc15f2c0f494f4b95f9185/e/5caa02e6b6557bf254634e34?renderMode=0&uiState=67057e8bf47da227d7580e21

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