I want to make sure you're able to manage your funds in QuickBooks. Just to clarify, are you using the Self-Employed version of QuickBooks? I'm asking about this because the Undeposited Funds account is currently unavailable in this version.
When you receive a check, you will need to record in the Transactions page. Any entry recorded is considered as deposited in your bank account. See this link for the steps to record self-employed entries: Manually add transactions in QuickBooks Self-Employed
On the other hand, if you're using QuickBooks Online, the steps to hold funds in the U/F account is easy. First, record the payment as a bank deposit then apply it to the invoice at a later time. Here's how:
Go to the + New icon and choose Bank Deposit.
Proceed to the Add funds to this deposit section.
Enter the customer name(s) in the Received From column.
Make sure to use Accounts Receivable for the Account so you can link it to the invoice.
Add a Payment Method then the respective amount you received. In your case, credit card.