It's actually rather simple, Lidija. After you finished your first overlay, just import it and dublicate it. Make sure that you select the second version and import a new overlay. When tsrw asks you, if you want to replace the current texture with a new one, say "NO"!!!!. That's the important thing. If you say yes, you'll overwrite your previous overlay. That's it, now you have two versions in one file.
If you want any more, just dublicate again, select the last version, import a new overlay and click "NO" when it asks, if you want to replace the current texture.