The custom field allows you to control, whether an invoice should be sent to the customer by Mobipaid. For Mobipaid to send the invoice, the custom field value must include 'yes' or 'y'.
In addition, Mobipaid will only send the invoice to the customer, if it has not been sent by QuickBooks. Therefore, when saving the invoice you should select 'Send and Close'. If you save and send, QuickBooks will handle the emailing, and Mobipaid will not.