Welcome and thanks for visiting the Community, @florinalazar.
There's no need to delete either of the transactions. If you'll write a check of the loan payment, all you need to is do match it with the bank transactions once uploaded. This will avoid any duplicates in your account.
For the category, QuickBooks records the loan/interest payment as a company expense.
Here's an article that will guide you on how to properly track loan in QuickBooks Desktop (QBDT): Manually track loans in QuickBooks Desktop. It also includes that steps on how to record loan payments.
I'm also adding this article for more information about matching bank transactions in QBDT: Add and match Bank Feed transactions in QuickBooks Desktop.
Please know that I'm only a post away if you have any other concerns. I'll be more than happy to help. Have a great day!
