Hi Pelu,
Here is the batch mode tutorial I was using for Registax;
http://www.astronomie.be/registax/previewbatch1.html
I typically process 500 - 800 avi's at a time and I found registax batch mode to be slow and unreliable. I started using Avi Stack instead it was much quicker, reliable and provided some good results.
I have not used Autostakker, so I can't comment on it.
Cheers,
Trent