Hay, hay, guys! I went to and edited Fircat's version of my set and added a few things and deleted the background around them, and guess what? It did not darken the background!!! I guess as long as I do not erase the whole background of the tileset, it will work. I also unchecked transparency in window, in Paint.NET. So, it's working so far.
P.S. Thanks sergiocornaga I'll check some out.