With multiple branding themes, you will be able to create more than one theme for each of your document types. You are not restricted to 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 customize 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 utilize this brand and the settings you have specified.
Ensure that you have allocated themes to your contact via Relationships. Documents about 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.
If you have multiple sales channels, you also have the option to assign a default branding theme to each of your sales channels.
Go to My Apps, select one of your sales channels, and from the Settings tab, you should be able to set a Default Branding Theme.