"... radio button on the customer's main screen that we can click to inactivate that customer..."
There is already a checkbox on one of the sections in the customer list for setting IsActive.
Checked = True, Unchecked = False.
"..Would it automatically inactivate that customer in Quickbooks or would we have to do it in both locations?.."
the sync should automatically update the change for you.
But keep in mind the sync is set up to work specifically with pre-created fields in method that have counter-parts existing in quickbooks.
If you made your own "Inactive" field, it would in no way affect quickbooks.
You must use the fields provided by method to affect their corresponding QB fields.
In this case you would use the Customer List's checkbox that exists as a Yes/No field in the Customer Table.
Hope this helps.
~Joe