If you are working with an airport that has enough traffic to warrant an overlay, such as KMSP, you'll want to make the runways active for both landings and takeoffs.
Designating one runway for takeoffs and the other for landings would not only reduce the airport's capacity to handle traffic, it would also defeat the purpose of using an overlay.
As far as ground traffic is concerned, you'll find that if AI is given enough route options for taxiing, the traffic in each layer should flow nicely (in somewhat of a circular fashion.) In other words, you might want to add an extra taxiway on the ramp in the vicinity of the gates.
Good luck
