@MLARN - I just did a little research for you and MediaMonkey will move your jpeg to another folder if you configure it in the options, the problem is that it doesn't support FLAC to ALAC due to licensing. Here's a work around that might do the trick if you don't find a more elegant solution:
1)Use MediaMonkey to send your FLAC albums with the jpeg file to another directory (maybe convert FLAC to WAV during this process as this happens in the middle of the FLAC to ALAC process anyway). You can set the output folder to retain your file structure/album folder title.
2)Use dbpoweramp or foobar or Easy CD-DA to convert your new WAV files to ALAC, but just have them save in the same folder as the WAVS.
3)I know Easy CD-DA has an option to delete the source file after conversion, in this case the WAV - OR just do a search for all WAV files through windows explorer and then highlight and delete them all in one move.