Yup, you got it... The clicker switch is an additional switch in series with the MagLite switch. You have to have them BOTH in the "on" position in order for the light to light.
I believe the idea (at least the manufacturer's idea) is that you leave the head focused the way you want (and consequently "on"), and use the tailcap switch to turn it on and off. I suppose it lets you hold it "tactical style" (I doubt that's the right term) and flash it with your thumb, too.
I had to use one on my MiniMag when I put the LS in because I put one of dat2zip's max1764 boards where the original switch was (Thanks Wayne!), thereby breaking the twist-on-off functionality. Without the tailcap switch, it's just on all the time
Actually, before I cemented the head in place, the twist-on and off still worked sorta. If I screwed the head down enough, it would push on the collimator, which pushed on the LS, which pushed on the max1674 board, which pushed on the batteries, which compressed the spring. The max board would move down away from the body and break it's ground connection and the light would go out. But, I figured it wasn't such a good idea to put all that pressure on the LS and circuit board, and bought a tailcap switch from BrightGuy.
-Kevin