@Brenda369 Steps 2 and 3 have some degree of overlap; this causes the issue you describe.
As a general rule, it's best not to use Journal Entries in QB unless you absolutely have to. If nothing else, Journal Entries do not play well with a lot of reports.
Instead, you have the option to take care of all of your needs in one deposit transaction.
In the first line of the deposit, for the From Account column, select the loan account you are using. Enter the full amount of the loan in the Amount column.
In the second line of the deposit, for the From Account column, select the appropriate expense account for the fee that a portion of the loan is being used to pay. Enter the amount of the fee in the Amount column as a negative value.
In the third line of the deposit, for the From Account column, select the credit card that a portion of the loan is being used to pay. Enter the amount of the credit card that is being paid off in the Amount column as a negative value.
This will have four effects.
The first line will establish the original balance of the loan.
The second line will lower the total deposit by the amount of the fee being paid while recognizing said fee expense.
The third line will lower the total deposit by the amount of the credit card being paid off while also lowering the balance due of said credit card.
The amount that remains after all deductions will then show up a deposit into the checking account you selected.