Now that we've taken a look at how to run NCover from the command-line and how to use NCoverExplorer to view NCover's output, we can take a look at the features in NCoverExplorer that allow you to do everything right from within its user-interface. If you click on the "Run NCover" button (the fifth from the left on the NCoverExplorer interface), you'll see this window:

If you click on the "Change..." button beside the Profiling application textbox, you'll see a windows like this:

Navigate to your test suite's Debug or Release folder for the Working Directory parameter, to the nunit-console.exe for the Windows or Console Application parameter, and the test suite dll for the Application arguments parameter. To continue our example, our window would have these parameters:
Working folder: C:\Development\Projects\NCoverExample\Test\bin\Debug
Windows or Console Application: C:\Development\Projects\NCoverExample\ThirdParty\NUnit-2.2.8-net-2.0\nunit-console.exe
Application arguments: Test.dll
Once you have this set up, go back to the Summary tab and click on Run and NCoverExplorer will run NCover just as you had been running it from the command-line. You'll probably see the coverage of your NUnit tests dll, too, which you more than likely don't really want, so you can filter it out by selecting it and clicking on the "Exclude this from Results" button (the one with an X on it) or by right-clicking on the node and selecting "Exclude this from Results".