Your basic problem is not a Perl problem, but a data modelling problem. You have a many-to-many relation between users and systems, so you should have 3(!) tables,
1 descibing users (id, name, etc),
1 describing systems (id, name, etc) and
1 for the relationship user_system (user_id, system_id)

In the users and systems table, id is a unique identifier for the user/system, which are used as foreign keys in the relation table.

If your data modle isn't sane, how do you expect your code to be sane?