How does it work?

[rstrauss-logyx]

I found the EcliPaint -> Icon Manager window.
I pasted my basic icon onto the grid.

How do I change white to transparent?

What do the 7 groups of commands do?

Are there any drawing commands or modes? Weird...

[jabiercoding]

You do not need the Icon Manager for this.
Right click the image in the project or package explorer and open it with the EcliPaint image editor. https://github.com/jabiercoding/eclipaint/wiki#image-editor

Then you can use the eraser to make pixels transparent. If you want to make transparent several pixels, erase one, use the color picker and select the transparent pixel, and then use the fill action.