You have an MP3 and you want to update the cover art with a lovely picture you downloaded. Here's a tool and a commandline to do that:
eyeD3 --add-image=cover.jpg:FRONT_COVER foo.mp3
where cover.jpg is the picture, and foo.mp3 is the MP3. This will do an inplace update of foo.mp3, adding the data in cover.jpg to the file. You can see the tag that was added with most v2 compliant id3 tools, such as:
root@bramble 4> id3v2 -l /data/mp3/misc/Bruce\ Springsteen\ -\ Dream\ Baby\ Drea
m.mp3
id3v1 tag info for /data/mp3/misc/Bruce Springsteen - Dream Baby Dream.mp3:
Title : Dream Baby Dream Artist: Bruce Springsteen
Album : Dream Baby Dream Year: 2008, Genre: Alternative (20)
Comment: Track: 1
...
APIC (Attached picture): ()[, 3]: image/jpeg, 5531 bytes