What shell are you using? Cmd.exe or PowerShell? With either one you should be able to run the .exe just by typing the name and hitting enter. You might want to put a Console.WriteLine("TEST"); as the first line of your app and see if it is printed to the console after you run your program. It could just be that the app is running and exits before printing anything.
LTM runs on a linux based operating system, so you won't be able to run a Windows executable on it. Generally, it's best to run management applications off of LTM to avoid unnecessary resources on LTM. However, if you do want to run an iControl app on LTM, you can using Perl instead of .NET.