Using a single ShockWiz device and swapping it between the front and rear suspension, is no less effective than using two simultaneously. The only disadvantage of using one device is the added time in tuning the fork and shock individually.
When using a single device to tune a full suspension bike, install and calibrate ShockWiz to the fork or shock and go ride. It does not matter which is tuned first, the end result will be the same.
Using the iterative tuning process, keep ShockWiz installed until you are satisfied with the Shock Tuning Score and feel of the suspension component. Then, install and calibrate ShockWiz to the other suspension component and again, keep ShockWiz installed until you are satisfied with the Shock Tuning Score and feel of that suspension component.
As a general note, it is always recommended that you create a Profile of the suspension component before removing ShockWiz. For more information on Profiles, see the Profiles - Creation and Use video.