If a single SQL server hosts multiple instances, how instances can be monitored under different profiles.
Currenlty only option I see is create unique user having access to single database instance. If you setup account with access to multiple instances. Test passes connection properties when server tab is set in stated syntax " hostname;database=dbname", but seems probe discards same while collecting the data as it shows data for all the instances.
If you are talking about different named instances, you can specify the server name using the following syntax in the connections tab: "ServerName\InstanceName".
If you are taking about different databases on the same instance, you can use Includes and Excludes for some of the monitoring checkpoints to define which databases you want them to apply to. For example, for one of your profiles, you could set an include on database_size to only monitor one of the databases. You could then set up a seperate profile to look at a different database.