It is Best Practice to manage all CSS, JS, Images, and other theme supporting files through the Web_Resources folder in your Percussion directory. Adding these files as Assets in CM1 may cause undesired results when previewing and publishing pages. Adding these files to your Web_Resources folder allows them to retain a static path and ensures they will be published live when a site publish is performed.
URLs to Assets and Pages are managed in CM1, allowing the system to update the path for an item when it is moved throughout the site structure. When working in the CM1 Dashboard, URLs appear as complicated strings with query parameters on them to allow the system to manage them, which is undesired for published links. When a site is published, the URLs for Assets and Pages are converted to reflect the location of the items within the site structure. Because of this, uploading theme files as Assets in CM1 will prevent them from being viewable in Preview and Published mode. Additionally, each time an item is relocated, the path in the CSS file will have to be updated.
As of CM1 v2.4, it is possible to manage theme files and other files located in the Web_Resources folder through the “Design in Finder” functionality. A new item has been added to the Finder to allow you to browse the Web_Resources folder to upload new files and download, edit, and overwrite current files.
More information on this functionality, including a tutorial video, can be found here: Design in the Finder.