For missing cover art with JRiver I do:
1. MKV file, I am not concerned about cover art as the MKV file on JRiver stores in the video section. The video files when split into chapters or as a whole plays the MKV music and/or video as it would if playing from a Blu Ray player.
2. When storing FLAC files of any kind, stereo, surround, etc, and the rip did not capture cover art, most of the time I go to Discogs, find the album cover, or disc shot, whatever, save image as, add to my desktop. Right click on album, click Cover Art, click Add From File, and done.
Many times, this action will embed in the file, so if you where to remove from your storage and put in another storage you may or may not get the tag.
Usually all the files I have that i add to a second storage, for safe keeping if I didn't get a captured cover art from the intial rip, then I will not have cover art in the safe storage, but I don't care it's always easy to grab cover art.
A note about Discogs cover art, most of the time when an album first comes out what is available are some shitty pictures, but if you go back a month later someone will have put up real nice pictures. Another good source for Hi Res music pictures is HR Audio Net.
Hopefully I answered your question adequately, you can PM me if you want.
I am sure other people do it the same as me or different than me, end result is all that matters.
