When you have a revenue item which you have to collect you should raise an invoice for it. This is done in the Application \ Invoice screen.
When you click on the New button the following screen is displayed;
Click on 
to move the currently selected item into the Invoice Revenue section and click on the 
to move all Unassigned Revenue to the Invoice Revenue section.
When you have added the revenue items to be invoiced click on OK and an invoice will be created.
You can then send the invoice out.