1. While there isn't an option within Graph Builder to generate CDF plots, you can easily generate your Graph Builder plot and then generate your Fit Y by X CDF plot, and since they appear in separate windows, you can move them side by side.
2. If this isn't complete enough, you can select the check box in the lower right hand corner of each of the 2 windows, and then click on the down arrow next to the check box, and specify "Combine Windows"
3. Or you can copy the windows a journal window. To create a new journal window go to:
File==>New==>Journal
The once the window is open, go to your Graph Builder window and click on it and then press and hold the Control Key followed by the J key. Finally, then go to the CDF window, and repeat the CNTL/J key strokes.
Now you can select and drag and drop the graphs to whatever position in the journal you want. Use the Tools from the Toolbar to select objects and then just click and drag the selected objects to where you want them
4. Finally, a JMP Script could perform these options for you, or a script could be written to generate the graphs from scratch and create them in whatever form you desire.
Jim