The easiest way to do this is by using the BiSym attachment for the Litegait. This device uses sensors in the yoke to not only tell you how much weight is supported, but also can tell you weight distribution between the right and left sides.
A low-tech, but not nearly as effective way, is to use a very thin scale and subtract the reading on the scale from the patient's total weight. The problem with this method is that even a fraction of an inch support (the thickness of the scale) can influence the body weight supported.
The important thing to remember, however, is that you should avoid using body weight support measurements for anything but documentation purposes. It is easy to become overly focused on %BWS instead of how the patient is responding to support. In other words, focus on setting the patient up with just enough support to allow for proper training--and don't worry about whether it is 10% vs 20%, etc.
The caveat to this, of course, is that you want to make sure you don't support more than half of their body weight, if possible. At that point, the patient begins losing sense of the ground under their feet and you'll get less and less muscle activation from them.
You can visit Litegait.com to see more information about the BiSym unit.