The custom controls in the application classes are designed to integrate with Visual Studio .NET's Visual Designer, and are used in the user controls (the ASCX files) generated by Iron Speed Designer. This means that if you open one of the generated ASCX files using Visual Studio .NET Visual Designer, you will be able to see the Iron Speed Designer custom controls, edit their custom properties using their property sheets, add them to your Visual Studio .NET Toolbox, etc.
The web controls in the application classes contain special .NET meta-tags in their code to enable this integration with Visual Studio .NET. You need take no special action to use these controls. These controls are already used in the web pages generated by Iron Speed Designer, so the web pages may be opened directly in Visual Studio .NET.