I think this would be pretty tough to accomplish. I think that PDFs have white backgrounds (as opposed to transparent ones), so if you were to simply lay the invoice over the letterhead, the letterhead would be covered up by the white background of the invoice.
You'd probably be looking at taking an invoice PDF, cropping it somehow to remove the white sections that would cover the letterhead stuff, converting it to an image, and placing it in the middle of a letterhead PDF. You might be able to do it with some Automator/AppleScript voodoo and Acrobat Pro, but I think it'd be pretty involved.
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