Yes, ERPLink will support Multiple Companies as part of the synchronization into a single database.
There is documentation in the user guide that will walk you through the process, but in a nutshell you will be creating additional templates for the additional companies.
One thing to note, there is a service pack for ERPLink scheduled for the end of the month that should address some issues with sync'ing. you may want to wait for that before making changes or installing.
