Alpha Channel in Photoshop question

K so, I was adding a few spots to the alpha channel in this skin, down near the bottom middle, at the bottom of the blade, you can see that the top one is:
with all channels active - a dark red
with all channels but alpha - black
with just alpha channel - a mixed gray

I tried to repeat the process on the next small part below the first one, only to find that I couldn't really remember how the hell I got it to turn out like that. If I just make the small section black, than add it to the alpha, it shows up as a brighter red, and I don't want that. I'm a newb with adobe photoshop, if anyone has an idea how to do this, I could really use a hand