To solve both problems, I would recommend creating your own theme for the SCLogin module. That way, when you upgrade the module or change templates, the settings will persist. For information on how to create the theme and then setting it in the module, see
www.sourcecoast.com/sclogin/documentation/themes
For the modal popup, please provide a specific URL where I can see it in action. If you don't want to put the URL on this thread, then please send me a PM using the envelope icon under my avatar. To fix the problem will probably just be some CSS that could be added to your custom theme. However, until I see it in a browser, it's almost impossible to know what to suggest to make it work with your template.
-Melissa