I use xrecode. It's pretty straightforward and you can point to the folder with all your flac and it can batch convert to alac. It's what I've been using to build my iTunes/iPod collection.
Edit: close iTunes and set the output directory as your "Automatically Add to iTunes" folder. If you have iTunes set to keep your collection organized then the next time it starts it will add all of your music and put them in normal Artist->Album->Song folder structure.
I've been converting all FLAC to ALAC for a long time. I love FLAC but ALAC is the same thing and compatible with my iPhone.
If you're on Windows I recommend xrecode3. I use it to convert all my files to various audio formats.
I'm not a technician but since I noticed that the new Plex player has some problems with the AAC created by ITunes I wanted to do this test. Normally I create my AAC with a program for Windows (http://xrecode.com/) that uses FFmpeg libraries but I have not noticed any gaps with your player
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xrecode III - the Holy Grail of audio conversion.
Xrecode has been my go to for multi-threaded audio conversion for years. It will defiantly keep your file structure intact, it allows bulk conversions of whole folders and sub folders, and is multi-threaded so it will do one song per core on your CPU.
Despite the official website, there is a freeware version available if you poke around on the net a bit. I will never use any other conversion program again.
Edit: couple this with MP3 Tag and you have a one stop shop for all your bulk conversion needs.
I bought a audio converter application for Windows, because once I wanted so much a game (Klonoa) OST and the asshat who did the rip encoded it in APE format with all tracks unified with only a CUE file to track the the soundtracks apart in the monster file, and I couldn't find a single good converter that did the job correctly, most of them or did a poor convertion or generated one big ass MP3 without any data to tell tracks apart. Then I found this one and it not only splitted the tracks apart based on the CUE file but also encoded them with the same bitrate of the pseudo-flac APE files, in the end even the ID3 tags it had put into the files and I ended with something like ripped directly from a CD. In the end I paid for that software and still using it today with my full love.
No one buys that kind of things but I did and I regret nothing.
I've been using http://xrecode.com/ with great success. Easy to use and can go to/from a lot of formats. You can donate, if you don't want to there's just a small splash screen you have to go through when you start it up, but it takes like 3 seconds and isn't much of a bother.