They don't think, they have a brain that allows them to drone on some task and to keep them alive(need brain to control heartbeat breathing etc), aside from that they are just shells.

At least that's what I get from reading Official and the intro.

No, but their mind is beamed to the brain jar, and the cortex commander (aka YOU) is beamed to the clone's brain. That is why you can still control them when your brain jar is destroyed!