@aleksandras2
OK, got it. I was confused since you mentioned deposits (plural). If you recorded it via a journal entry (debit cash, credit loan payable), that increased both your cash balance and your payable. Therefore, you can either match the bank deposit or exclude it.
On the second part of your question, do I understand correctly that you made payments to a vendor, that were charged to a credit card, and those payments are reducing the loan payable? Unless I'm not understanding, you can just enter a credit card charge and assign the charge to the loan payable account. That will increase your cc balance due and reduce the loan payable.
