Payment made thru quickbooks, why do I have to manually enter the payment?

I get 2 emails in succession: Payment scheduled and Payment on the way. It's great, I can see who just paid me, for how much, and which invoice they paid. After all, they did all the clicking to get me that info.

A few days later a deposit hits my account, same client, same total. But because there are 2 invoices to them, with the same total. The system needs me to match it. 

I find this to be asinine! They paid a quickbooks invoice, using the quickbooks system, shouldn't everything that has happened until now tell that very system which invoice they paid? It's all connected! What am I missing? Why doesn't a quickbooks payment know which quickbooks invoice was paid? 

The lesson I just learned is, every time I get one of these emails saying someone has paid. I then need to go through the process of receiving a payment from that client to the invoice they paid so when the deposit hits my bank everything matches and this completely automated process when wholly untouched. 

Am I wrong? What I thought was a completely automated process from beginning to end is truly a manual process and was never going to be anything different? 

Why doesn't quickbooks know what invoice was paid when the payment was made thru their very own system?

I've got 80+ clients who get monthly recurring invoices that rarely change... so this is about to become a very big issue for me.