I want to create a custom application that sits within an existing umbraco website. The custom application has nothing to do with the website and will have all of it's own functions and views.
I would prefer it to be on the same host web deployed, but if this is not possible I will create a separate app and host it on it's own sub domain.
EDIT:
Okay so after reading this again, I realized this wasn't being phrased very well.
So what I wanted to do, was have an umbraco website, and then build a separate web application and host it as a virtual application within the umbraco website on IIS, the default setup didn't work, so I am assuming umbraco is eating up all of the routes and then not being able to detect it, gives me the page not found error.
I eventually opted for just hosting the application on a sub domain as it's own website in IIS.
If you want a completely separate application that has nothing to do with the Umbraco website and its going to be hosted on a sub domain.
Then why do you need/want it to be connected to your current Umbraco site in anyway.
Just create a new blank MVC project and host it on its own, then point your subdomain to your new app.
If the two applications are loosely related, you could create a new project in your Visual Studio solution it will not effect your current Umbraco installation.