Ah yes, that was an earlier and much more crude hack. That's remarkably simple: just change the background color of the bottom screen at any time. Since the screen is being drawn at the same time your code is running, the results literally show up in realtime.

A huge downside with this technique is that color changes during H-blank (waiting period between scanlines) and more critically V-blank (rather long waiting period after each full screen draw) cannot be seen. When I was using this technique, I had the engine actually wait until all of V-blank had passed before it started doing the timing colors. This still ended up being pretty hard to read of course, as the colors would change flicker rapidly at 60FPS, couldn't be easily saved to view later, and were complicated significantly by the multi-pass nature of the engine, where each visible frame is actually composed of several hardware frames, all with totally different timings. So I scrapped that method almost immediately and wrote text-based profiling code that used the built in hardware timers.