"I guess I’ll have to keep doing what I’m doing or change my Windows password every time I change my iSeries password."
That is exactly what we advise our users to do. In fact, when users change their iSeries password we automatically send an e-mail reminding them to change their windows password to match.
About 50 users in our company have shared drives on the IBM i. In our case, we share an IFS folder where data warehouses live.
As long as users keep their Windows and IBM i passwords in sync, all goes well. Of course, the same user ID is also a requirement.