Ok, that is a good solution. I've used paint.net before, but for some reason its layout didn't jive with me. I'll try it for this problem though. Thanks!
EDIT: grrr.... yeah, I can't figure out how to do anything with paint.net. I should be able to select all the tiles I want, delete them, then re-fill with the correct transparency and color. I'm just using single colored transparent tiles cut into various shapes. Instead, it deletes the marque selection.
I'll keep trying, but if anyone has another suggestion, please let me know.