If you go to “Configure | Alarms”, then select the “Custom Counter” (either Windows or SQL Server), you can see “Default Severity” in the dialogue which opens up and next to it an “Add” button. This button allows you to specify a severity type, which is the name of the custom counter. Spotlight will distinguish these as different alarms with their respective severity and they will appear as different alarms in the log.
Also you want to add a severity to the severity type then added the following value to the descriptions:
{{key}} has a value of {{value}}
Where
{{key}} = Custom counter name
{{value}} = Custom counter value