A few months ago, the .NET SDK was released in the archive. Have you had a look at it? (Package name is SDK_DotNet.) I am not sure if it includes its own documentation or if the CodeWizard has been updated to produce sample code.
You can always use the nimqos.exe command in the bin directory to send QoS from any process/script regardless of the language. I do not think you should have to do that in this case, but it is an option if you have any trouble with the SDK. Just make sure you create a QoS definition before sending any QoS data. (There is a command for that too.)
QoS tracks only one measurement for each point in time. You will have to decide what makes the most sense for your probe as far as source and target. (You probably need to define a new QoS type specific to traceroute.) I would probably make the host running the traceroute the QoS source. For the target, you can choose between hop number, hop IP, destination IP, and a combination of those values. Just be careful because IPs can move around in the list if there is a change in the route.
-Keith