The Password Utility has nothing to do with SYS user . It's to create the SYSDBA's password . Note: Sysdba is different from DBA . It's much higher priviledge and basically he can do everything in the oracle ( shutdown , recovery etc )
DBA user's job scope is much narrow .

So SYSDBA's password is stored in password file and DBA's password is stored in the system table .

Only one password can be used . You have to delete the previous one I think .