I have the CPX with two batteries. This is the way it works...
The battery indicator in the LCS display shows the load of the highest load one (in percentage). At the same time you can see the load bars for both batteries.
For example... I charged both bateries at 100%. As the 1st battery is used... its bar decreases but the 100% remains on the display as one battery is not used. In the app you can read the real ammount in batery, for example 160% when one batery is full and the other is at 60%.
When one battery reach the 20% of load... the CPX automatically switches to the 2nd battery and the load start decreasing... the display now indicates the load of the 2nd battery (81%, for example).
When you charge the empty battery and install it again into the scooter, the CPX continues using the battery with less charge. With this method you always use both bateries equally, I mean both batteries are going to be used the same number of cycles from 100% to 20%.