I think I understand what you're trying to do. Try this:
1. Create your square out of Color 1.
2. Draw your circle within your square using a contrasting Color 2.
3. Select both the circle and the square drawings
4. Ctrl - X to delete
5. Edit > Paste Special > PNG. Now the image will appear as a single PNG
6. Select the image
7. In your picture toolbar (which will be highlighted because you've
selected the PNG above), find the Set Transparent Color icon, select it
8. Click on the color 2 inside the circle - it will disappear and you will
have an empty circle shape within a square.
Also there is probably a way to do this using the underlying image as your
Background...
