Good question, deronisabel.
The process is the same. You still need to write a check when funds for the loan are transferred in QuickBooks Online. Simply enter the EFT in the Check # field when you record the payment.
You can also visit again this page: Set up a loan in QuickBooks Online. Then, proceed to Step 3: Record a loan repayment. It provides instructions and detailed steps on how to enter the loan made via an actual check or electronic payment.
Stay in touch with me if there's anything else you need about your loan. I'm always right here to help.