I have another option on how you can do this in QuickBooks Desktop, Kryler.

Normally, we recommend paying the credit card at the end of the reconciliation. You can continue the payment by writing a check. To do so, follow the steps outlined below: 

1. From the Banking menu, select Write Checks.
2. Select the bank account you want to use for paying the credit card from the Bank account ▼ dropdown.
3. Select the date of your payment.
4. Select the name of your credit card company from the Pay to the order of ▼ dropdown.
5. Enter the amount of your payment.
6. Select the Expenses tab.
7. On the Account ▼ dropdown, select your credit card account.

Once done, your payments and charges show up in your credit card register and you'll be able to reconcile the account in normal process. 

To know more when paying credit card charges after reconciliation,  there are 2 options that you can do to pay a portion of the outstanding balance. Check out this article for more information:  Set Up, Use, and Pay Credit Card Accounts.

However, I still suggest reaching out to your accountant if you want to use the journal entry so you will be guided on what accounts to use. 

Furthermore, learn how you can add and match bank feeds. This article will give you three modes available that you can. Go through this article for more details: Add and Match Bank Feed Transactions in QuickBooks Desktop.

You can always post your comment below if you have any other concerns when paying using credit cards. I'd be happy to help.