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Yes, since there is a new checking account that is created for the loan, you can select that when you're about to record the payment.
Here's how to record a loan payment:
You'll need to enter the payment, interest, and bank fees as separate line items in the Category Details section.
To enter the loan payment:
For more information, please refer to this article link: Make a loan payment in QuickBooks Online.
I've also attached here a helpful article that can help you in managing your loans in QuickBooks Online: Loan in QuickBooks Online.
If there's anything else I can help with, feel free to post down below. Take care always and have a good one.