Do this to create Transparent logo/spray for css.
It's really that simple.

Use Counter-strike to import the TGA logo you just made..
Don't MAKE me give you a tutorial on that...

EVERYTHING YOU DO... DO IT ON A NEW LAYER!
This is so that the  image can be adjusted in any way you want.
Create a LAYER SET, and store extra copies of layers you might want Back-ups of (EVERYTHING if you are me).
Use Layer Sets to organize the layers...lettering in this folder... images in that folder... clan symbols in another folder, etc..