I know the title doesn't make much sense, but I was wondering if it is possible to overlay one sheet on top of another during a takeoff?
For example, I want to take off the control joints on the structural plan but only certain new areas, for which I need to reference the partition plan.
Hi, you could try our page Overlay tool. I'm not sure if it does everything you need, so maybe you could test it and let me know if you have any questions.

https://www.zztakeoff.com/community/product-updates/new-update-overlays-duplicate-project-break-apart-linear-rotate-point-counts-etc
This is exactly what I was asking for thanks. Is there a way to hide the overlay but keep it attached for later?
Yes, there is an eye icon button in the highlighted row below that toggles an overlay's visibility.

ah, thank you, I didn't think to look there