Specify different logo for a Custom Theme

No not the logo on the logon page that has been done years ago. Please the objective is to use a different logo for a particular customer invoice. Now this can be done by selecting your custom template for the invoice. So all that needs to change is logo for that particular invoice.

How do we specify only a logo change in the custom template given we have the image name and compatible image size etc available?
Just feel we should have some clear directive as to the most efficient way of achieving this task without digging deep into html code.

Access to the resources location will allow us to change the favicon.ico as well which is another thing I wish to do with this white label product.