I'm going to show you my method of applying transparencys I don't know if everyone does it this way or not but it works for me.
Start off with your image that you want to have transparencys I'll use the GC thug logo. Open it up in photoshop and make sure it's on a transparent background.
It should look like this.
All the spots that are checkard is what we want to be transparent, if yours are still white click on the magic wand tool and click on the white and delete it till it resembles the image above.
Right click on the image under layers and go to duplicate image
A box will appear, click the drop down box and select new.
Now you'll have an identical image, make sure you have this one selected and go down to the layer box, and right click on the image and go to blending options.
In blending options menu click on color overlay so it checks the box, you want to apply an overlay of WHITE.
Hit ok and everything that you want to appear in game should be white.
Now make sure your background color is set to black,
Then click on Layer in the menu bar at the top and selecet "New layer from background".
now the image should look something like this
If so good, lol, push control A to select the entire thing, then control C to copy it, now return to your original image, and click on channels, click new layer
It will make a black box that says alpha channel.
and then control v to paste in what we just copied.
Should look like this
Just save it as a TGA file now and import it into CS.
I do it this way because this is how it must be done for animations, but for a still pic it works as well.
If you have any questions just post em here.