I use motion builder, its awesome, really easy to use and all in realtime.
I the main process is to link the joints names together so that the data can go form the mocap to the skeleton's heirarchy.
So the generall motion builder workflow is to make the skeleton and skin in maya, export into MB then characterize the maya character with a motionbuilder character, linking joints and making your naming converntion match MB's then you can add a FBIK or straight mocap, or blend the two.
MB's got a lot more under the hood too, facial animations etc etc.
"No pressure, no diamonds" Thomas Carlyle