If I'm understanding this right then what you're wanting to do is call a custom tool you've already written from a menu instead of a toolbar. When a custom tool is on an ArcMap toolbar, ArcMap handles activating that tool for you when the button is clicked. When you call it from a menu, then you have to handle the activation yourself. If your custom tool is on a toolbar, then all you need to do is call IDocument.CommandBars.Find to get that instance of the tool and set it to be the current tool using IApplication.CurrentTool. If your custom tool is not already on a toolbar then you will need to create a new instance of the tool class, call ICommand.OnCreate and then set it to be the current tool using IApplication.CurrentTool.