Not sure what OS you are running your Scan to Fax function from but in Win 7 the Microsoft Fax and Scan wizard can accomplish what you want. This free app will allow you to craft a fax message like an email. All you need to do is save your fax template somewhere on your machine and then insert the text or attachment on a new fax message. Once your cover page is attached then attach the scanned job and shoot it off. Easy peasy if you dont mind the extra few steps to attach everything.
Another soluion would be to scrap the physical faxing service and migrate over to an online fax vendor. Online fax allows anyone to manage fax documents through thier favorite email client. That way you can have custom templates, signitures and whatever else you want just like you would normally be able to do for email. The biggest advantage is that you only need access to a scanner to manage your faxing. Get your jobs into a scanned document and let the online fax vendor handle all of the physical sending and recieving for you.
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