Unfortunately, there is not an easy way to do this in the Windows Forms designer. You have to go to the form code and change the XYPlot constructor call in InitializeComponent to instead call the constructor for your custom plot.
I have customized plots too. If you want to see them in the designer (in the "Edit Plots..." section) you just have to add your plots in the waveformplot collection editor and then manually change the class name in your code to the name of the class you want to use.
The designer wont complain at all and you will be able to see the plot in the list as if it were a waveformplot plot. Moreover your new class properties will appear in the designer in the waveformplot collection editor.
