I see that I can pay bills using the "Direct Payment" method, but I can't do the same thing when paying employees. Is there a work-around to this? I want to prepare an EFT through my bank's web interface, but I don't know how to handle paycheques on the QB side.
You can do everything you want with VersaPay (see their website).
Process payroll in QB as usual, just when create paycheques, select "Assign cheque numbers to handwritten cheques"; you may set "EFT0001" as first cheque number. Then print out paystubs to hand out or email to employees.
In your bank web, enter net pay for every employees via EFT module.
