It seems like there isn't a solution for your problem, even in the brand-new Power Tools 1.2 for QlikView. QV User Manager lets you configure the QlikView Management Service but from there on it automatically finds all attached QlikView servers.
Maybe if you start two QV Management services and configure two User Managers, each with it's own configuration file. But then you'll have to disable management of both installations from a single QMC...
Hmmm, maybe you can ask this question in the PowerTools 1.2 discussion or suggest an improvement to Stefan Bäckstrand?