Application form and fee for Drupal Commerce
The new line item type and adding it to the order was the way to go it seems.  My code is posted in this post.

That code worked, however, I kept getting an access denied when trying to check out. DC runs a hook called hook_commerce_checkout_order_can_checkout().  The order is passed to this hook, and you can determine if you want to allow access.  I did on all instances and didn't need to write any logic, so I just returned TRUE, and everything worked.