Anyway, back on topic...

Although the two CV inputs have different legends they are almost functionally identical. They are simply the two CV inputs for the two VCA that are wired in series. So you can swap the cables around and it will work the same.
The legends underneath the sockets are different only to aid in understanding what a patch is doing. So if you want to change the fade in point, for instance, then you know which cable to re-route. But it's just a convention.
Here's what's happening in the patch...
Red = Part 1 fade in signal
Yellow = Part 1 IS ACTIVE signal
Green = Part 2 fade out signal
Cyan = Part 2 IS ACTIVE signal
Magenta = final audio signal
The IS ACTIVE signals gate the fade signals. In other words when low they turn the high fade signals off. In a minute I'll knock up an illustration just to make it completely obvious, then move on to how to fix the glitch.