I have logged a request for this feature in SiteAssist Pro, thanks for the feedback.
As for hte problem you are having with the mystyles it should make use of the same file regardless of weather or not you are working on the index page or any of the other pages that are derived from a template. If you look at the reference in the index page it should appear the same as the references on the pages derived by the template. The location of this file should be:
import url("siteassistpro_css/mystyles.css");