Okay, you have worked out how to put your logo on your transparent button in photoshop, I use photoshop CS2, hopefully it's the same, otherwise this advice may be less than helpful.

You need to have the layer's box open, your transparent button will show as layer 1, when you put the graphic over the top of the transparent button a new layer 2 will appear.

Double click on this layer 2 graphic and it will open a layer style box.

Use the 'this layer' slider at the bottom of this box to remove the white background. Some experimentation may be required here by using the 'blend if' dropdown menu which is just above as it can make some difference, also you may have to experiment with the graphic itself bu using image-ajustments-levels (topMenu) to brighten/darken the graphic you wish to use, do this before adding your graphic to your transparent button.

hope this helps, Adam.