Very glad to hear about the lack of murder. :) But the brain stuff involves the process of synchronizing the mind of the pilot and the Jaeger, allowing the pilot to seamlessly control the Jaeger's movements. It's called 'Drifting,' this process. You ever watch any of the Star Treks? It's a mind meld, basically.
Originally, a pair of pilots was needed to control a Jaeger because the sheer size of the machine and one brain would just get fried in the process. But we're down grading to half the size, so that it's more of a one person mech suit. Iron Man, but bigger and badder, no partner required.