I also have the exact same question.  Is anyone able to assist with what MDR12 has described?  It has been two months since asked.  

I️ am trying to understand why when I️ send an invoice to a customer and they click the invoice to pay the invoice via their credit card - I️ receive a confirmation a payment has been made which is great, however the funds are not being posted to my bank account they instead go into Undeposited Funds.  I️ do see that undeposited funds are defined as a holding spot for funds that have not yet cleared.  So my QUESTION is what happens with those funds?  Do they get appropriately posted to the corresponding invoice# once their bank clears the credit card payment? Or am I️ supposed to do something with them?