Direct deposit is a safe and convenient way that allows you to pay your employees. Funds are deposited into employees’ bank accounts directly through an electronic network rather than through a physical, paper check. The following are the basic steps you need to follow to get started.
Direct Deposit Setup Process:
With the above setup, you will be able to pay employees with Direct Deposit as follows:
Select "Company" from the top menu and click "Edit Company" to launch the company edit dialog. Then select the "Direct Deposit" tab. There are three sections, one for each record type in the deposit file that need your input with information about your company and your bank. The following is the screenshot for record type 1, also called the file header record.

The fields above with notes to the right are pretty self-explanatory. Here are some more tips on how to fill them out.
Note: The notes to the right of each field above shows the position of the field in the record of the direct deposit file. It can be useful if you need to inspect the generated deposit file before you upload it to your bank.
The next section of input fields are for record type 5, the batch header record. In most cases, they should be the same as the corresponding field for record type 1, unless your bank provided you with different values.

The next section is needed only if your bank requires that you submit a balanced file. In such a case, make sure that the "Create Balanced File" checkbox is checked and the following fields for the offset record are filled out.

To pay an employee through direct deposit, the employee has to be enrolled for direct deposit. To enroll an employee, just select "Employees" from the top menu, find and select the employee from the list, and then click the "Edit Employee" button. The "Direct Deposit" information is in the "Direct Deposit" tab. It looks as follows.

First make sure the "Enroll in Direct Deposit" checkbox is checked. Then fill out the bank account information. A void check from the employee would help fill out the information.
After you have done the company setup for direct deposit and enrolled your employees, you can start to pay your employees through direct deposit. First, you run payroll as usual and create paychecks for all employees worked in the pay period. Then select "Direct Deposit" from the main menu. The paychecks for all enrolled employees will show as "Outstanding Transactions"

If your bank requires a balanced file, make sure the "Generate Balanced File" checkbox is checked. A pre-note file is a direct deposit file with zero dollars for all payees. It is for verification purposes. If your bank requires that you send a pre-note file before you pay any employees for the first time, you can generate such a file if you select the "Generate Pre-Note File" checkbox.
If you need to exclude an employee from a direct deposit file, just uncheck the checkbox for the corresponding record in the transactions list.
Once you are ready, just click the "Generate Direct Deposit File" button to generate the file. The default location for the file is
<workspace>/<Company Name>/Direct Deposit
where <workspace> is the workspace directory that you have specified when you ran the initial setup. If you have forgotten where it is, you can click on the gear icon on the main menu to launch the setup dialog.
Finally, you may upload the file to your bank.