I am amending my state taxes to add the rental deduction. How do I get the software to uncheck that I am filing a federal amendment, I'm only amending the state.

To amend only a state return:

https://ttlc.intuit.com/questions/2824532-i-need-to-amend-my-state-return

Ignore the federal forms ... they are inconsequential and do not affect the already filed return.   In the FILE tab choose to mail in both then only mail in the state. 

Normally that is what I would do. However, I had unemployment and it is forcing a federal amend. The IRS has stated amendments were not needed, but the software is automatically creating a federal one. I selected to mail in and also went back to select to not file it right now. Both times it automatically has the box checked in my Indiana saying yes I am filing a federal amended return. Is there a way to uncheck that box? Or can I just use whiteout and then mail it in?

Again ... to amend the state the federal must also be changed (even if the IRS will make the correction automatically)  so it is reflected on the state return ... it is an unusual situation this year.