Just to clarify is the negative bank balance in a Square account or a regular Bank account?

Are you instantly transferring money from Square to a regular bank account that is negative?

If so it won't have any effect on the Square transfer as they are just depositing money into the negative bank account, however depending on how long your bank account has been negative how the bank handles it is a separate issue.

Most of us have been there and the hard choices we make in running a business makes things tricky sometimes. Best of luck, I know negative accounts can be such a hard climb to get out of because sometimes they're negative because of the overdrafts for being 0.1 negative!