For modifying the CSS, please make sure you've read through our
Joomla Login Theme Guide
. That describes the best way to override our styles (or create your own) so that they aren't overwritten when you upgrade.
Similarly, for the PHP files, you should use the Joomla template override system. To do so, simply copy the /tmpl/login_vertical.php file (for instance) to:
/templates/<YOUR_TEMPLATE>/html/mod_sclogin/login_vertical.php
Then, edit the new file you just created. That will be used instead of the original file from the /modules/mod_sclogin/tmpl directory.
The only thing to be aware of is that when you upgrade the SCLogin module, you should compare the changes in your override to the new, original file. There may be changes you have to incorporate into your override to use new functionality or simply to make things work properly.
I hope that helps explain, but if you have any questions, just let me know.
Thanks,
Alex