Hierarchical Select Doesn't allow multiple vocabularies in drupal7
You can't I'm afraid; it's actually a limitation of the taxonomy term field type, not of Hierarchical Select.

You can only ever choose one vocabulary per term reference field, regardless of the widget you're using. For example, this is what the field settings page looks like when adding a bog standard term ref field on a Drupal install that doesn't even have HS installed:



As you can see you only have the option to choose one vocabulary.