richnyc30
There's probably a language issue. For example, I don't understand what you mean by "uncompress a CSS file." Perhaps you're referring to minification?
Adding a new CSS file that will be recognized on all pages of the site is simple. You need to add two lines to the template's index.php.
$document = JFactory::getDocument();
$document->addStyleSheet('templates/your_template/css/mycustom.css');
But the index.php file, like the template.css file, is overwritten with every template update.
Only the custom.css file remains unchanged even after Joomlart updates in the future.
That's why I'm telling you to only use custom.css to add changes. But, again, maybe I don't understand what you're asking. Are you worried that the custom.css file will become too large? Or difficult to manage?
If these are your concerns, know that wherever you put code, it will impact the site, no matter where you put it, whether you add them to one file or another doesn't change anything. Secondly, when you insert code into a CSS file, you can add a comment to remind yourself what it's for. In other words, any CSS changes, whether to the template or to JCE, can be added to custom.css. If you do this, your changes will last for years and won't be overwritten by an update.