I'm dealing with the same issue here, but I'm wondering bout the excluding option. Here's my scenario: 

I received an ACH payment through an emailed invoice (quickbooks payments processed it), and it automatically matched it to the corresponding invoice. But, a payment takes a few days to disburse, and now I have a transaction that's importing from my bank. Because it's already been processed and matched automatically, do I exclude this transaction? I never have needed to do this before. The only thing that is different now is that Quickbooks Payments put the deposit into my savings account instead of my checking account. I think QB expected the transaction to be in the checking account, and maybe that's why it's not showing up as a transaction that I could match it to? 

Any suggestions would be helpful.