You are able to pay an invoice with multiple forms of payment. In the below example we'll use part card and part cash. Keep in mind that you can use this same process for multiple cards as well!
Here we have an invoice for $160. We'll pay $100 with cash and $60 with a Visa.
Hit Take Payment/Pay.
Check the Pay box for the invoice.
In the Amount Paid column, change it to $100.
Choose cash as the payment method.
Hit OK to save the receipt.
You will be back on the invoice and it now has $60 due.
Hit Take Payment/Pay.
Check the Pay box for the invoice.
Choose Visa as the payment method.
Hit OK to save the receipt.
If you search for the invoice in Accounting, Receipts, it will show both payments attached to this invoice.