how to identify and reconcile deposit on my bank statement to the online payments?

I am considering moving to Quickbooks online payments.  I would need to process a couple hundred invoices at the 1st of each month.  They are all the same amount for each customer.  So when doing the reconciliation at the end of the month, how would I know which deposits to my bank account tie to the auto generated deposits in quicbooks?  I can’t envision how this would work.  There is typically a delay between the time the customer processes an ACH and the time it hits the bank account and multiple ACH payments on the same day don’t always hit the bank at the same time.  It just seems like it could be very difficult to reconcile.  I am a one man show so I need to not make this a bigger problem and more work for myself.