You can use a custom Order Printer Templates document design with the PDFs generated for customers, to give them a more professional and branded document.
Note: This guide does require you to have purchased a Order Printer Template design first.
Login to Order Printer Templates (Shopify admin -> Order Printer Templates)
Click the "Installation instructions" button on your purchased design
Copy the template code
Login to Order Printer Emailer (Shopify admin -> Apps)
If you have previously setup the app before then click "Edit emailer", otherwise click "Create emailer"
In step 1 of the setup wizard, replace the code in the field "Template code for document" with your custom template code
Complete steps 2 and 3 in the setup wizard. If you are updating an existing emailer and have followed the steps before, then you can skip this.
Now each time the PDF is generated, it will use your custom template design.