I am trying to monitor a server with APM v2 that has the default instance of SQL Server disabled. There is a non-default instance of SQL Server 2005 running on the server but I don't see in the new v2 SQL Server template (or old SQL Server template for that matter) where you can specify a particular SQL Server instance. Using the default v2 SQL Server 2005 template gets me healthy indicators for the SQL Server processes but everything else is either reporting unknown or down.
I ran into the same problem. I eventually discovered you can use the AppBuilder wizard to connect to the SQL server and list the WMI counters per instance name. Once you get the WQL you can create a new monitor or cut/past the WQL into the monitor within your SQL template.
This worked for me. Thanks