Using one ShockWiz, 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 that 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 record the settings of your suspension before removing ShockWiz. This includes; Baseline Air Pressure, Number of tokens/ bands installed, and all current damper setting positions. These settings cannot be stored in the App, and it is recommend that a page for each component be created in your phone or tablets "Notes" app.