This tip augments the tip Change Your Icons. That tip is for changing individual icons (including folder icons). This is a special tip for changing your folder icons system-wide.
Select your new Icon, right click on it and navigate to Add-Ons | Filetype. Leave the FileType window open.
In Tracker, navigate to /boot/beos/system/Tracker and open its FileType add-on.
In the Tracker’s Supported Types list, select the Folder entry.
Drag the image from your new icon’s icon well into the Tracker’s Folder icon icon well. Hit Alt+S to save and enjoy!