When viewing the invoice in Housecall Pro, scroll all the way to the bottom where the QuickBooks card is. Click the 3 vertical dot menu in the top right corner of that QuickBooks card.

Click the $ Add local payment option.

If you do not want the customer to be notified of this payment being marked, then uncheck the Notify customer option.

Enter in the amount of the payment you want to mark as paid, then click PAID - CASH.

This is how the payment will look in HCP:

Note: Creating a local payment will mark the invoice as paid in HCP, and will not push over a payment to QuickBooks.