The system allows you to not only add multiple eBay accounts but also to manage them with unique invoice templates and from email account settings.
To achieve this you will first need to create custom invoice template sets by going admin > custom invoice template sets > Add New Document Template
You can then create email and company alias so each ebay store looks independent of the other.
The Invoice / Order Template is the only one that needs to be customised as it is used as the email upon order dispatch from the system.
Once you have created a new document template set you assign it to your eBay account by going ebay > setup > store manager > clicking relevant ebay account > selecting new document template from drop down.
To customise the actual template logo you will need to clone the email templates by accessing the files as per following screenshots:
In the below examples the default.template.html file has been cloned and renamed ebay.template.html
Note that the file name must end with .template.html for it to display in settings above.
Once you clone the above templates you need to change the image name to new logo by accessing the html code below and changing it to new image you have uploaded:
Upon completion of this step you go back into document template set and swap to new template file: