In the projects settings "Debug" section there's a textbox for "Command line arguments:". When the VS debugger starts the C# program, it'll pass those arguments to the process just as if the program had been started form the command line with those arguments.
The alternative is to use a command line debugger. There are a few options here, but in all honesty they're probably not what you want to use instead of VS unless you're getting into some really hairy debugging scenarios. If you're interested in checking them out, there's a good summary in this SO answer:
You can also try the techique of putting a call to System.Diagnostics.Debugger.Break()
early in your initialization - if the program is running under a debugger, it'll break, it it's not running under a debugger you should be asked if you want to attach one. You can make the call conditionally depending on a configuration file or environment variable setting so you only get the break if you're really interested in it (somewhat intrusive, but not too bad).