My workaround (also annoying) is to create a Bill for each ACH Payee.  Then, when the ACH payment in QBO shows up, I chose Find Match and it often picks exactly the right "Bills".  Much easier than Journal Entries AND as far as I can tell is ok for 1099's as the Payee is properly identified.  

But yes, QBO, you do need the option to Split a Transaction to Multiple Payees, not just multiple categories.