To configure the Auto Invoice extension please login to you Magento admin panel and navigate to: System > Configuration > Magmodules > Auto Invoice.   

Auto Invoice

1. Payment Methods:
elect the payment methods that need to be invoiced automatically. You may also select multiple payment methods. Selecting multiple options will vary in different operating systems and browsers:

For windows: Hold down the control (ctrl) button to select multiple options
For Mac: Hold down the command button to select multiple options.

Change Status.
Select if you wish to change the status of the order.

Set Order to Status.
When you activate this option, you can select the status where it needs to be changed.

Add Comment.
Select if you wish to add a comment to the order when the auto-invoice functionality is used

When you activate this option, select the comment you want.

Send Invoice Email.
Select if you wish to send an invoice email to your customers.

Ship Order.
Select if you wish to automatically create an option for Shipping for the order.