Paypal is a bit tricky, because you are sending the user off to "pay" for the order. So Kentico doesn't really know if the user pays or not. You can configure it though to put a different status when they pay with paypal, and then update it afterwards. Check the Store configuration and the Payment options, there should be a drop down to set the Order status for each different payment gateway.
As for the 2nd item, I Know you can use macros in the subject and body, but I believe you can also use Macros in the to/from as well. Go to Email Templates, set the site to Global, and you'll see the ecommerce emails there. Try modifying and adding your logic that way. If that fails, may need to do some custom hook interception on the email objects getting created, but that may be a pain.