Being in the military (Infantry in particular). I have spent a great deal of time dealing with this concept.
I think what you are trying to train is the ability to have the "two brains" work in harmony.
We train in the Army to make things such as putting your weapon on your shoulder, breathing, arming and firing an automatic response. One that needs no thought...it just happens. That is reptilian so to speak.
By training these things to be automatic, it frees the brain up to think about things that are important such as who I am pointing my weapon at, where my troops are, and what is the next course of action I need to pursue.
I am also taking a course in leadership and decision making on the master degree level right now. It is very interesting to see that what science attempts to label with fancy words, that what Aikido and eastern arts have figured out long, long ago!!!
Our preceptions, paradigms, and our experiences serve to either help or hinder us depending on the situation.
To make good decisions we must constantly try to step out away from ourselves and train hard to make sure we have a good understanding of ourselves and our environment.
I think aikido does both....it trains the reptilian brain, and it trains the conscious brain to work together.