Yes Visual Styles Modules can be used even if your template uses a proprietary template engine such as that used by YooTheme.

However keep in mind that YooTheme doesn't use and follow Joomla templating framework, in this case although it's possible using Visual Styles Modules some features in the Modules Dashboard could differ. In particular the reordering feature can't be used and menu modules can't be dragged in the Modules Dashboard.

If you are unsure about the working mode of Visual Styles Modules on your YooTheme template, contact us asking a trial copy.