Mongo, after you compress the layers (flatten the image) you need to save it as a gif file.
File/Save for Web. When the dialogue box opens, choose "gif" and make sure that the "transparency" box is checked. You will see a split image "preview pane" which allows you to preview your original image in comparison to the image as it looks, based on the 'save options' that you choose.
There's lots to learn in this area and, although you're going to experiment with the different settings, I would suggest that you check out this tutorial first
http://www.wise-women.org/tutorials/ps1/
Good Luck!
