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If you are receiving deposits on a loan you made, it is not a loan payable, it is a note receivable. Make sure you have a note receivable asset account set up. The journal entry to record the loan would be to debit note receivable and credit cash for the amount of the loan.
When you download the bank transactions, you can add them or match them if you have entered them already, or exclude them. You need to split the payment between the note receivable asset account (principal portion of the payment) and interest income account (interest portion of the payment). This will increase your cash balance, reduce the note receivable balance, and book interest income.
I'm not sure I understand the last part. Can you explain in more detail? Did you loan money to a vendor and fund the loan with a credit card charge?