1. Bring your skinned mesh into motion builder and apply the rig.
2. Add a character extension to your character and assign the root joint. This is so it will be plotted with the rest of the skeleton. Assign a reference object to the extension (hips?) and update the stance pose.
3. In the root joint properties enable degrees of freedom and set translate Y min to 0.
3. Add a position constraint to the root and assign the hips effecter as the source.
I line them up by disabling the y on the position constraint, activating it to place the root in the x and z, then hit snap so it maintains the offsett then enable Y on the constraint. Be sure to set to lock.
4. At this point the root will follow the hips but not penetrate the floor. The distance between the hips and the root will be maintained when translating the character off the floor. This can be adjusted using the position constraints translate Y in it’s properties (you’ll have to unlock temporarily). That way you can adjust at what height the hips have to be before the root will begin to raise of the floor.