Yes, CSS in your template will remain even when you upgrade, which means that it should always stay where it is.. unless we make big changes to the SCLogin module, which aren't currently planned.
Glad we could help get you going, but should you have any other questions or issues, just let us know.
Finally, if you haven't already, please consider leaving a rating and review for SCLogin, or our support, on the Joomla Extension Directory. It certainly isn't required, but is very appreciated:
extensions.joomla.org/extensions/access-...authentication/24054
Thanks,
Alex