I would suggest the following:
Drag the cover art files you want to import to Playing Now. Press Ctrl+A to select them all and do a right-click import. While the files are still selected give them an unique tag in AW>Tag, e.g.
Genre: Cover Art.
You can exclude this genre from your regular image view schemes and use the same tag for creating a smartlist of the files.
Related question, some covers are in another location. If I go and find them all and move them all into Application Data etc. will MC see them?
Not automatically. "Cover Art > Quick Find..." can do that if the filenames follow the "Album Artist (auto) - Album.jpg" naming rule. If the cover art files files are named differently it would be better to leave them as they are. Alternatively you could use the "submit to..." and "get from internet" tools.