I'm not sure of the program you speak of but I just manually add them to my music files in iTunes. I just download the album cover and them to to files.
This may not work for you, but that's what I do. Yeah I know I could download from iTunes but I just do it manually since I don't log into iTunes Store becaue I never use it.
Anyways I'm not sure this helps you, I just thought I'd throw it out for an idea