ExpressID AFIS allows you to store application-specific data without modifying table structure. There are two ways to do this: tags and custom data string. Both are described in IDKit PRO SDK under section Notes.
If these features are not enough, you can create your own application-specific tables and link them to AFIS tables through user IDs. Adding fields/indexes to AFIS tables is also possible although use of separate tables is a cleaner design.