@ kmgdesign: There are some options to change the logo on JA Puresite template. You can consider two simple workaround below rather than creating a new file called custom.css:
1. You can look for the h1.logo a {} css block in the template.css file and add your expected logo as the background image.
2. Another option is to open the templates/ja_puresite/blocks/header.php file, and look for this lines of code:
<a href="<?php JURI::base(true) ?>" title="<?php echo $siteName; ?>">
<img src="<?php echo 'templates/'.T3_ACTIVE_TEMPLATE.'/images/logo-trans.png' ?>" alt="<?php echo $siteName; ?>" />
</a>
Then replace the declaration in red with the path and alt info of your logo image. Remember to clear JAT3 cache after updating change.