Let's be clear on this first:
With disks you really mean physical drives, i.e. you have three drives, two of them with OS X, one with Windows?
And one bug to know about:
Chameleon 2.0 RC1 offers you to boot from any drive and its partitions it can find. However, if you try to boot Windows on a different drive than where Chameleon was started from, it won't work. But let's not worry a about Windows here.
So, assuming you have two drives with OS X each, you can check if Chameleon (i.e. a boot loader) is installed on them by telling your BIOS to boot from it. If it doesn't boot, it has no boot loader on it. Also, the volume will have a file called "boot" in its root dir.
Next, should Chameleon load, it will either show you a graphical or a textual message (and it will show its own name or icon so you know it's Chameleon), counting down to let you know it's about to start up some pre-chosen OS. If you press a key, you get a list of partitions you can boot from.
And if you get to that list of choices, BOTH your OS X systems should be offered to boot, provided they're both connected.
Hence, if you have Chameleon on either of your disks, you should be able to boot either OS X volume from them.
Once you are running OS X, launch the ".pkg" version of Chameleon to let it install itself on the active OS X volume, and maybe add other extensions to its Extra folder then as directed in other posts or guides.