Changing somthing's color pixel by pixel

It blows my mind that somthing this simple isnt all that simple. I used the eyedropper tool to slect a color from another photo, then used the brush while fully magnified to change the color of each pixel. It was coming out a weird greyish color, and I noticed that if I clicked more than once, it got darker, but so did the pixels directly around the one i was editing. So, i copied both pictures, loaded them into paint, and went to town. It worked, but then when i copied it back into photoshop, it had a black background (there was no background in the original pictures) around the sprite I was editing. I tried to use the magic wand tool to get rid of it, but it took parts of the sprite with it, so...

Is there any way that I can edit the color of a single pixel (or hell, even a group of pixels if they share the same exact color would be nice...preferred, even) accurately? If not, what program could I use that would keep the transparent background?

I hope this was specific enough. Thanks.

Yeah you need to use the 'pencil tool' rather than the brush if you want to paint one pixel at a time. Set the size to '1 pixel' and make sure the mode in the tool options bar is set to 'normal'

If you want to save transparent areas for other applications to use, you need to save in a particular format, depending on what application you are going to use. I'm no expert with this, but if you're saving for web use, try the GIF format.