You can modify the icons by adding your new icons to the share/icons/crystal-admin/ folder, and creating variations for each of the size as appropriate.
When you need to add a new one to work with a custom class, you need to create an icon.ini override in your admin siteaccess settings folder, to override the original icon.ini in the share/icons/crystal-admin folder. Add a new line with the class identifier and icon file name.
From the header of the ini file...."It is not recommended to edit this files directly, instead a file in override should be created for setting the values that is required for your site. Either create a file called settings/override/icon.ini.append or settings/override/icon.ini.append.php for more security in non-virtualhost modes (the .php file may already be present and can be used for this purpose)."
However, you should take a look at the original icon.ini to see the structure and options available.
You need edit the override in admin siteaccess for icon.ini file. For examples about useful configuration directives see: share/icons/crystal/icon.ini.
<i>ClassIcons</i> and <i>ClassGroupIcons</i> assign icon files for content classes and groups content classes respectively.