You can create additional HTML Templates which can be used for Email Templates. Navigate to Administration->HTML Templates.
Select the Create Template button.
In the Create Template page set a name and then in the HTML tab you can set the HTML code that will configure this template.
The Options tab allows specification of which type of content this template is to be used for.
Now when configuring an Email Template you can use the Template option to select which of those configured is used for this email.