I have the same or similar issue...  QBO automatically records deposits and applies payments to invoices.  When I go to the banking screen to add/match transactions downloaded from my bank, the matching invoice doesn't show on the list.  I have to delete the deposit (created by QBO), then the invoice will show up on the list to match with deposits... So it appears the solution to my issue to stop QBO from creating deposits.  HELP!  HOW DO I DO THIS!  Any other suggestions are greatly appreciated.