You need bits of a parent for a clone.
If you want to keep both the parent and the clone, which may be necessary for some games

, then you should probably build a custom list in your frontend - adding only the version you think is "best."
If you only own the clone version of the rom (the best version) and you want to get rid of the the parts of the parent that you don't own, then you just have to move the files from the parent rom which are required by the clone rom to the clone rom's zip archive (or folder). Then you should be able to delete the parent zip archive (or folder) and your clone should still be playable.
If you do that with all your best roms then:
available games = best games
for most automatic frontend game list builders and full rom list audits.
oh crap.. I just reviewed the "easy on me" part of your post , sorry, heh.