To access icons that will appear to everyone on the server just right click on your server name in the TS3 client when logged in as Server Admin and you will see "View Icons". Click "Upload" locate your custom 16px x 16px image ( png, gif, jpg) and click "Open". You will see your icon under the "remote" side of the Icons manager.
Next to specify these uploaded server side icons with the permission "i_icon_id" "Icon identifier", Under the "Permissions" editor in the TS3 client. For example go to server groups locate the "i_icon_id" and then click to change the value. You will notice that a window appears showing what icons are available. Choose the icon you wish to use and whenever an individual is in that server group they will be identified with that icon.
It also might be better to follow this guide: http://tserverhq.com/tut/createicon/start.htm