TGA files and masking

Hi everyone. I am new to these forums and have come up against a barrier in a mod that i am making for an old game (Wizardry 8) which uses tga graphic files for all its textures.
I don't seem to be able to make a file with both opaque and transparent texture in it.
Example would be a leaded window where i would like the window part fully opaque (i say leaded but actually it would be gold)
I know this is something to do with masks and the Alpha channel but i have not figured it out.
When i blank out the window part then the other colours in the image become semi-transparent and if i don't i get black window that i cannot see through.

Could someone tell me or point me to a thread that explains how you get a transparent background while prtecting the rest of the image from any kind of transparency ?

It's ok. I have discovered how to do this now