If you use Adobe Photoshop as your external editor, you will discover that it places an icon's mask in the alpha channel. While it is possible to modify it there, it is much easier when it is merged into a layer as the transparency data. This pair of actions allows you to easily do this. To load them into Photoshop, locate your Layers palette (you can show it from the Window menu). Then, using the pop-up menu from the upper right corner, load the file contained in this folder. You should have a new category in your Actions palette entitled "Iconographer Actions."
To use them do as follows:
1. Export the icon from Iconographer using the "Open In External Editor" command from the Icon menu or the shortcut you selected
2. Run the "Alpha to Layer (when starting)" action
3. Edit the newly created as you see fit (if you create more than one layer, make sure to merge them back to Layer 1)
4. Run the "Layer to Alpha (when done)" action
5. Save the file in Photoshop
6. Switch to Iconographer
7. Preso! Your icon should be updated with the changes you made in Photoshop.
Note: this action set has currently been tested only with Photoshop 5 and 6, it is not known whether it will run with other versions.