To have your header and footer showing on documents, you can set up all your templates to include the header and footer coding in those sections. If you ever need to change your header and footer details, it will be easy to just upload the new images as described above, and all coded templates going forward would generate with the new header/footer.
On each template, click into the Header & Footer section, and using the Template Designer, add the code for 'Header Logo' showing under 'Matter' fields.