merging two systems

I have two systems that both use freeradius out of MySQL. I would like to consolidate onto a single system, but maintain the database separation to ensure there are no username collisions and ease in auditing/reporting, etc. System A already has a database of freeradius_A and system B has a database of freeradius_B. What is the preferred method to configure freeradius to authenticate two sets of users out of two databases? Should I look at running multiple instances of freeRADIUS or can I utilize both databases with one instance? --Blake