I think what you're looking at is the invoice displayed when you first click the invoice tab on an order? That is all drawn from customer.itpl.php, it's just that your site's style sheet is being applied to it. I didn't add a stylesheet to the template by default to keep it e-mailable. However, you can easily add a link to the stylesheet yourself.
At least I think that's what's happening. If that doesn't explain it, feel free to post some screenshots.