With multiple branding themes you will be able to create more than one theme for each of your document types. You are not restricted on the number of themes you can create.
Go to Settings> Identity and Branding. You can click Create a New Brand if you wish to have multiple brands.
For each brand, you can customise the settings for the documents, as well as emails. For more details, click on this article.
By checking the box "Make default brand", all your documents and email templates will utilise this brand and the settings you have specified.
Ensure that you have allocated themes to your contact via Relationships. Documents pertaining to these companies will then be assigned the allocated theme rather than the default setting.
Go to the Relationships section via your main app manager.
Select your desired company and click on edit. You will be able to set the theme for the contact here.