I hereby post the text I used on a ticket I just created. I'll probable get a reasonable suggestion from Kaseya how to do what I'm asking. What I'm also wondering is the smart ways others choose to do some SQL performance monitoring, so nay suggestins or tips are appreciated:

We use classic monitoring to monitor performance on SQL servers. We didn't check this very actively, since it's only used for a bit of troubleshooting and we don't create alarms based on our monitoring. We 'discovered' today this monitoring doesn't work on SQL servers with named instances. Which isn't a big surprise, just something we didn't bother with or even realize was going on.
We roll out SQL performance monitoring based on SQL views, with selects on all labels with active SQL versions, through Policy Management.
This scenario leads to the question if we can create a default monitorset for SQL Performance, that takes into account different instances? We now notice counters disappearing for instances because the Perfmon counter names don't match. I found Traverse can be configured to monitor these instances without too much trouble. How can Classic Monitor be configured with Policy Management to take into account different instances?
We can see two ways. Either we create a policy exception for every single SQL server with a non-default instance. Or we add lines to the existing monitorsets for all the instances we find and count on Kaseya Monitoring to remove all lines that don't match (which seems to work, but I'm nt sure about). This would result in a very large number of lines, with a predicted number of instances in the dozens. I'm not sure that's a stable and rational approach.
We'd like to hear your recommendations about this situation....

As a side note today is the day we finally noticed/realized Kaseya doesn't yet has a label (in Views) for SQL 2017, which is annoying (and the subject of another ticket). It can't hurt to be aware of this.