Control Stand ?

On a lot of pictures of Alco control stands that I have seen there is a second handle\lever in the same "track" as the throttle. It is a smaller handle and is located behind the throttle itself. What is it's purpose? It's not the reverser, which is below the throttle. The only thing I can come up with is dynamic brakes perhaps?

You're describing the selector handle. The Century series manual I have explains:
1. Handle in "Off" position disconnects traction motors, power and braking circuits.
2. Handle in motoring position no. 1 sets up motoring circuits. Transition will take place automatically both accelerating and decelerating.
3. When in MU with units equipped for non-supervisory automatic transition the selector handle in the lead unit should remain in the No. 1 transition position.
4. When in MU with units equipped for supervisory automatic transition, the selector handle on lead unit should be placed in selector position No. 4.
5. When in MU with units equipped for manual transition, selector handle should be moved from position No. 1 up through position No. 2, 3 and 4 according to operating instructions on the locomotive equipped with manual transition.
6 . Handle in braking range provides control of dynamic braking. If locomotive is not equipped with dynamic braking, a stop on the controller prevents movement of the handle into the braking range.

Transition is basically the changing of traction motor connections (e.g. series-parallel to parallel) with regards to load and speed. The first event is apparent on DC units, where the engine returns to idle for a second or two, I'm thinking around 20 mph.