Upper / Lower Body run animations

Hey guys, I haven't been able to figure out how to play one lower body animation for running forward
and then play a different upper body animation depending on the situation.

For instance, the bottom half will always be the legs running, but the top half would be the arms
swinging (normal run) or holding onto an item while running.

So that would be two different upper body animations for run.

I know you can use the .cfg file when exporting the animations to isolate
particular parts of the body, but how do you tie that into the run animation?

Thanks much for the help!