Thank you all for your response. 

Its an overdraft line of credit attached to same business checking account that is connected to my QBO. I agree, that as I use the limit the bank balance will go negative and I shall incur interest on used amount.

For example, I have $100 balance in my checking account and I pay a supplier $150. $100 of this payment will be my existing balance and $50 will be the credit that I receive from my bank. After this payment my balance should be -$50. 

This is one transaction but this will be an ongoing process. How should I record above transactions and will I have to manually differentiate between credit from overdraft limit or my own balance every time? 

I hope I am able to explain my question better. Please help!

Thank you!