I agree with GRJ above. I like the manual controls. In fact I installed manual controls first and have never bothered to automate them as I usually walk around while running trains and like having the manual switch controls at the switches. However, I don't have the Lionel command switches, was going to use an AIU.
I would at least leave the manual controls connected until I got some train running/operating in to see which method I preferred or whether I liked having both available.