In patch mode, the CTL button is programmable, (as is the expression pedal) and you can have it set to activate, de-activate or change a ton of parameters at once, either in toggle mode or as a momentary switch (the effect only stays active while you're standing on the pedal). The CTL pedal is also used for the tap tempo when you've got delay or tremolo effects that have their time base set to tap input.
Yes, the GT-6 can be operated in manual mode.
http://www.bossgtcentral.com/pics/gt6frontbig.jpg
Press the "Manual" button and the four pedals operate as Preamp, Overdrive/Distortion, Delay and Chorus. I would assume you can assign the CTL pedal to turn another effect on and off, or use it for tap delay tempo. But i never, ever use it in manual mode because in my opinion, the GT-6 is far more powerful in patch mode.
By the way, there's a GT-8 apparently being announced at NAMM this month that adds some new stuff to the GT-6 like amp control and dual amp model capability, and it also re-arranges some of the effects. They've moved the compressor out of the FX-1 group and made it a standalone effect, as it should have been from the beginning. Wait a few weeks and the GT-6 will probably drop in price, and/or you may be able to find some cheap ones ones on eBay as people upgrade. Or if you want the features of the GT-8, that'll be an option, too.