There was a new blog post about exactly this today: Application Insights Support for Multiple Environments, Stamps and App Versions.
The destination of the telemetry is determined by the instrumentation key (iKey), which is sent along with every telemetry message. In the Application Insights portal, similar events and metrics with the same iKey are aggregated to give you charts of average durations, event counts, the sum of users, and so on. The iKey appears in two places in your project. One is in ApplicationInsights.config: <InstrumentationKey>94843456-2345-3456-4567-324562759284</InstrumentationKey>
If your application has web pages, the iKey also appears in a script in the head of every web page. Usually, it’s only coded once in a master page such as Views\Shared\_Layout.cshtml.
To direct telemetry to different application resources, we can create several resources with different iKeys. Then we only have to change the iKeys in the application at each transition in its lifecycle – along with other configuration data such as connection strings, certificates, and subscriptions.
The article then goes on how to do this in code, confg, etc:
1) Add iKey as a property in Web.config:
2) Instead of using the iKey from ApplicationInsights.config, we’ll set it in the code. In global.asax.cs.
To avoid confusion, remove the <InstrumentationKey> node from ApplicationInsights.config.
3) Configure the web pages to pick up instrumentationKey: "@Microsoft.ApplicationInsights.Extensibility.TelemetryConfiguration.Active.InstrumentationKey". This is the script usually found in View\Shared\_Layout.cshtml.
4) Don’t forget to update your Web.config with appropriate iKey configuration during the deployment process. You might devise a way of setting it appropriately as part of your build, but I’ll leave that to you.