[quote user="Philip Attisano"]I don't understand how I can connect to a specific instance of Microstation if multiple instances of ustation.exe are running[/quote]
The short answer is: you can't.
[quote user="Philip Attisano"]_app = new BCOM.ApplicationClass();[/quote]
You're using COM to find MicroStation. COM can't distinguish between multiple instances of the same application. This isn't a MicroStation issue: it's a general issue with COM. Search MSDN and other web sites that deal with programming issues to see similar questions and possible resolutions.