I do not understand your problem.
If you set the trigger to index change, AutoIndex can obviously only know about the document where the index changed and will use only this document. However, you can still have this job trigger for a lot of documents simultaneously (if you change index entries of all the documents you want).
I think you need to describe in more detail what you want to achieve with AI here for us to help you.
Greetings from Germany,
Simon H. Hellmann
DocuWare System Consultant