Sorry it took so long for someone to respond!

To answer your question:  Yes, you can use the same active runway for both layers, but the ATC for each layer will not be aware of what traffic is doing in the other layer.  Thus, you might see two aircraft landing on top of one another or two aircraft taking off simultaneously on the active runway.  Not very realistic.  If you're planning to use overlays at all, it's best to make the active runways different for each layer, if possible.

Good luck

No..........not really.

You need at least two runways to do an effective overlay.  It helps if the runways are positioned so that traffic can be easily divided into two sectors at the airport.  It also helps if the runways are aligned so that incoming and outgoing traffic doesn't conflict with traffic from the other layer.

Perfect example would be Minneapolis St. Paul Int'l (KMSP.)  You have two parallel runways located on opposite sides of the terminal, 12R-30L and 12L-30R.  Using the overlay technique, you can split the traffic half-and-half between the two runways.  But since each runway will be active for landing and takeoff, THEY WILL BE BUSY!  To be honest, this would simulate real world traffic at KMSP.

Good luck

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