I am not very knowledgeable about this mod and I got it pretty recently. Is there an option to replace blocks with blocks from the schematic instead of just not building there. Thanks.

There is a pasteReplaceBehavior option in the Generic config category. You can also quickly cycle the value by default with Ctrl + M, and the current value is show on the "tool HUD" on the bottom left when you are in the Paste mode.

Tysm I tested it and it works!