Ext.NET is C# or VB.NET code for the behind code (mostly server-side) of a website. Ext.NET generates ExtJS JavaScript using a .NET library, and that then creates the user interface elements. In Ext.NET, you have a collection of controls parallel to the ASP controls that can be added to the aspx files, and you have a library of Ext.NET commands for C# or VB.NET that can be used to create and manipulate those controls. So basically, if you want to use Ext.NET controls, you should create an Ext.NET project in Visual Studio and migrate the C# behind code and markup from the old project to the new Ext.NET project, and gradually replace any ASP.NET controls that you want to be replaced with Ext.NET controls.
Does that help you any?