Basically most of the work that happens automatically after the post payment verification in the event of confirmed payment will need to be manually done for manual checkout. The reason is that the plugin has no way of confirming a manual payment.
In your setup you said that you don’t care about payment confirmation so you can probably do all the post payment stuff in the manual checkout code. Simply have a look at the “paypal.php” file (around line 401) and see what it does then you can copy some of those code.