EFT currently exists for paying accounts and invoices (bills) by selecting the Bank (Online) option - see attached image.
The use of the word 'CHEQUE' is simply a naming convention that goes back to the beginnings of the application. You can in fact think of the CHEQUE form as any payment method (EFT, Petty Cash etc...). In essence... it simply records money leaving a particular bank / asset account.
Payroll is a little different. If the employee has a Pay Method of Bank (Online) in their employee record, the payment will be sent to the Online Banking Centre automatically when the pay is created.
TIP: To avoid seeing a cheque number on the employees paycheque, in the Review and Create Payment screen > select Assign cheque numbers to handwritten cheques > type EFT or Direct Deposit (or wording of your choosing - no numbers) in the text field for First Cheque Nu...
This method can also be used any time a cheque number is requested however you do not want the transaction to be send to the Online Banking Centre for payment with an ABA file. eg. Pay Bills by cheque.
Summary
This is good but it is a pain to have to type it in every time. I would prefer to see a drop down box with options as we have Chq account, Everyday savings account and Visa Debit transations.