Hiya. It onlly uses one output because the device I'm connecting it to is itself a sequencer. The sequencer only needs a clock pulse to tell it how fast to cycle, and then goes about it's business.

I'm working on another project that will be more simple and have 1:1 control, but strangely this was the easiest thing for me to do with the kit at the time.

So, I think your understanding is correct, I just used a rather weird example that may be confusing.

It's a modification of an old black & white TV, most often called a "Wobblescope" from Nam June Paik's popularization of the technology. There's an instructable on how to build your own here: instructables.com/id/How-To-Make-A-CRT-TV-Into-an-Oscilloscope/