If by 'multiple' you mean 'independent' galaxy instances, they must each talk to independent backend databases, so if you're thinking of running eg 2 or more independent instances at CSIRO, each for specific tool sets and sending each of your users to one or other of them based on some smart Apache code and their login, beware that users won't be able to share or see any histories or datasets from one instance on the other. 

That might work well - or not - but separate instances cannot safely share the same backend database tables - they're just separate Galaxy instances - like test and main are, and there's no specific documentation needed.