Hi there, amit6.

Thanks for the sharing additional clarifications to your concern. 

To make sure everything is aligned, you may reach out to your financial institution and verify if the fifty dollar is a principal line of credit or pure overdraft.

If your bank claims that this is a Line of Credit, you can perform the process I have shared above.

If its an overdraft, you can follow Rustler's recommendation and record it as a regular expense transaction and the enter the payment as a deposit.

Regarding your question on how to record the transaction, you'll have to manually differentiate between credit from overdraft limit or own balance every time.

I'll be right here if you have further questions. Keep safe and have a good one.