Within SiteAssist Pro if you alter any of the pages that are derived from the template then any changes you make to the editable regions will be retained. However, this is not the case with the index page. This page is recreated every time that you make a major change to the site. You will not be able to overcome this using the mystyless.css file. You will need to keep a copy of the old page and copy the content back into the newly created one.
The mystyles.css file is used only for the styling. If you have some custom css that you would like applied to areas of the site then you would want to store those style definitions in here. This way they will take precedence over any other styles even with the same name. Also, when you modify the site this mystyles.css page will remain intact.