Hi xentryx
You can use various templates in your site, if you want to combine another template with JA Builder, there are 2 ways when you create new menu item:
1 - If that menu item has type of normal Joomla content like: Articles, Contact, etc... and you assign that different template, it will show normally (everything will from that template). In case you assign JA Builder to this menu item, the Header + Footer blocks will be from JA Builder, the main content will be content of menu type.
2 - If that menu item has type of JA Builder page: everything will show from JA Builder if you assign JA Builder template to this menu. In case that you assign different template to this, Header + Footer will be from that template, the main content will be blocks of JA Builder.
I hope this makes senses.
Regards