The way I have done anything with a transparent background would be to first make the graphic and make sure you can see the gray and white squares signifying that it is indeed background.
After you see that, go to File > Save As.
Name your file whatever you want and right below the File name box, click on the drop down list and chose “CompuServe GIF (*.GIF)”.
Click “Save” then on the next window you can keep the Palette to Exact, Forced: Web (or whatever colors you need)and make sure “Transparency” is checked off. Matte can stay at none.
Click “OK” and it is saved with a transparent background.
I hope this was what you were looking for. It should be able to import into any program you need without a background.
Always Start with the End in Mind