NCover Support here.
If you are using NCover Desktop, you can auto-configure to detect any .NET code that is being loaded by your testing (Bolt can only profile test runners).
We have this video that shows auto-detecting NUnit, as an example: http://www.ncover.com/resources/videos/ncover-creating-a-new-code-coverage-project
And a lot of the same info in this help doc: http://www.ncover.com/support/docs/desktop/user-guide/coverage_scenarios/how_do_i_collect_data_from_nunit
Please contact us at support@ncover.com if you have extra questions. Hope this helps.