You can set certain properties for RadEditor by modifying the respective ConfigFile.
Web Part and WCM scenario
You need to modify the ConfigFile.xml which is located in the following folder:
/Program Files/Common Files/Microsoft Shared/web server extensions/wpresources/RadEditorSharePoint/5.x.x.01f131a624888eeed/Resources/
For example you can set the ImagesPaths property here:
<property name="ImagesPaths"> <item>/SiteCollectionImages</item> </property>
The same approach is used when setting FlashPaths, DocumentsPaths, MediaPaths etc. properties. If these properties are not set, by default RadEditor will load all local libraries (local to the current site). For more information, see Image Manager
SharePoint forms scenario (Lists, Wikis, Blogs, etc.)
You need to modify the ListConfigFile.xml located in the same folder.