FitNesse. UserGuide. DotNet.
First, you have to tell FitNesse to use an alternate COMMAND_PATTERN, formatted specifically for the .NET FitServer. To do this, add these lines to the wiki page (on the Edit Page):
!define COMMAND_PATTERN {%m %p}
!define TEST_RUNNER {dotnet\FitServer.exe}
!define PATH_SEPARATOR {;}

The classpath should be modified to list the .dll files that should be loaded. Use the !path widget for this:
!path dotnet\*.dll

And, if you have a config file for your application, you can tell FitNesse to use it with the !path widget as well.
!path c:\path\to\my\project\MyProject.config

Here is what that looks like when the page is rendered (not including a config file):
variable defined: COMMAND_PATTERN=%m %p
variable defined: TEST_RUNNER=dotnet\FitServer.exe
variable defined: PATH_SEPARATOR=;
classpath: dotnet\*.dll

These are the paths needed to execute the SuiteAcceptanceTests, which uses the .NET FitServer to test the .NET FitServer!