You should go to EShop -> System -> Configuration -> Layout tab, fill in the [PAYMENT_COMPANY_NAME] tag to the Payment Address Format and [SHIPPING_COMPANY_NAME] tag to the Shipping Address Format, then they will work as your expect.
I added <br />[SHIPPING_COMPANY] into the Shipping Address Format so that the company's name is shown in the shipping address in my order confirmations and invoices. However, this inserts a blank line in orders without a company name. Is there any easy code I can add so that this blank line is suppressed (e.g. if [SHIPPING_COMPANY] is not blank then insert <br />[SHIPPING_COMPANY])?
My shipping address format currently reads as follows: