I recently caused myself major problems trying to convert a large karaoke song library to lossless - mainly through ignorance.
The conversion process crashed part way through. I then discovered that the converted files and some copies of the originals were being stored on my local drive - away from the external drive that houses my collection, and not where I was expecting

To make matters worse, I also managed to trash an extensive iTunes collection.
Worse still, the backups that I thought I had carefully and regularly taken were hopelessly out of date.
Only a fairly recent Time Machine backup and Dave's patient advice saved the day (Thanks Dave!).
After a lot of help from Dave, and his suggestion of using File Synchronization utility to merge two partial song folders in the unconverted state, I am now back up and running, with a 95% of the karaoke songs I had before, iTunes restored, but a lot more grey hairs!
Whilst helping me, Dave suggested making an alias to the song folder on external hard drive in my internal HDD Music folder, which also contains the kJams library. This enables me to check my backups by creating a further alias to the backup folder and temporarily substituting the new alias for the original alias to the main collection by simply renaming. This is probably the most valuable lesson I've learnt from this experience.
I would like to restart the conversion process to Apple Lossless, but am now extremely wary. I need to avoid again compromising my original song collection - so I intend to do this from one of the backups on an external drive (using the alias trick).
However, can anyone please advise:
1. How to ensure that the conversion takes place into a specified location, preferably separate from the source folder, and also so I don't end up with a mess of folders and files on my internal HDD, etc?
2. Dave mentioned that zipping files is a good idea and saves some problems with file names screwing up. I hadn't previously zipped anything during ripping because I thought unzipping would be an extra process prior to playback. Can anyone who uses Apple Lossless comment on their experience of this?
3. Also by setting the 'zip files when ripping' option in kJams preferences, will this apply during file format conversion?
Thanks for your help,
- G