This feature is similar to one known as "table switching" that you may have used before on other systems except that instead of just switching the tables, the entire tune is switched. The only exceptions to this are physical constants that there is only one available copy of.
The primary copy of all switchable items is enabled by default and is normally what you want to adjust while tuning the engine. It is also what is in use when the tune switching mechanism is enabled and not engaged. The secondary copy of a given switchable item is enabled when the tune switching mechanism is enabled and engaged. If tune switching is not enabled then the secondary copy is never used.
Although this boils down to paranoia, some precautions are best taken when tuning your vehicle with FreeEMS. Because there are always two copies of all settings and the code has the ability to switch between them you you should always configure the secondary copy explicitly.
If you are not using the tune switching feature it is wise to configure all values in the secondary set to be exactly the same as what is in the primary set. This way if you have tune switching turned on by accident and the input pin is floating you will not get erratic engine behaviour.
When adding things to the set of switchable data please ensure you insert appropriate default values in both the primary and secondary copies.