(1)
If the second window is called win2 then you can access the PApplet object with
win2.papplet
You stop/restart the auto redraw or change its framerate use

1. win2.papplet.noLoop();          // stop autodraw
2. win2.papplet.loop();              // restart autodraw
3. win2.papplet.frameRate(5); // set tghe draw at 5 fps

Note that if you use noLoop() then the window will not respond to mouse and keyboard events, if this is required then set the frtamerate to a low value e.g. 4. I used this in the Mandelbrot example that comes with G4P because it creates multiple windows (I have had at least 20 open at once) it reduces the framerate on each inactive window then increases it again on a mousePressed event.

(2)
All the global variables used in the main sketch are accessable in the draw method for the second window. So you can change the values in the main program and these can be used by the draw and event handkers for the second window. If you want the second window to have it's own data then look at the simple windows example (comes with G4P) and read about it here.

HTH