Coming from QB Pro I have always used my banks (Wells Fargo) bill pay feature through QB, now that I have switched to QBO I cant seem to get it working - all I see is Bill pay with bill.com at $2 per check
QuickBooks Online uses a different third-party program for paying bills online, dugonline.
The Online Bill Pay feature in QBO is powered by Bill.com. This program works differently from what QuickBooks Desktop uses. There is no monthly fee for using this service, however, there's a transaction fee for each payment you process.
Were you submitting – ACH-NACHA file to Well Fargo Bank to process direct deposits? If so, you can do that using third party software. Please check Intuit Apps center - https://apps.intuit.com/app-b7rhf97pmg - Customer Payments / Vendor Direct Deposit by ACH/NACHA. Once the vendors banking information is setup, you can generate NACHA file using the paid bills in QuickBooks, without any further data entry and associated errors.