When you make the loan, post the check to a new other asset account, for example, Jones Loan. This will record the loan and it will appear on your balance sheet as an asset. When Jones makes a payment, you can record it as you deposit the payment into your checking account. Go to Banking, Make Deposits and fill in the deposit slip. Received From Jones, Account Jones Loan, and the method of payment and amount.

You can go to Lists, Chart of Accounts at any time and double click the Jones Loan and see a register showing your loan or loans to Jones and his repayments