The invoice system is designed to encourage direct file editing, but I would encourage you to make a copy of the invoice template and work from that copy instead of just editing the default. (This way you don't accidentally overwrite your work on an update!)

Because you can use any PHP in the invoice template, I'd encourage you to use node_load() to load up your custom node as referenced by the order's products and display that info in the invoice.

You can use this link for now to view the invoice system documentation:
http://64.233.169.104/search?q=cache:Gx8r8FynKmoJ:www.ubercart.org/uberc...