Hi, thanks for the answer.
The project is supposed to remotely monitor a parking space.
The two sets of batteries because the Arduino MKR GSM 1400 needs one battery for the GSM communications (if I am not mistaken 
) and the second one is to power the Arduino itself.
As I need this system to be fully autonomous, I added a solar panel and a solar charger for each one of the batteries and because the Arduino needs to be powered up on 5V, I added a power boost too.
I might be completely wrong but I thought it made sense at the time
The application will be to monitor the parking space as I said and then update a database with the status of the sensor.
The GSM is included into the Arduino MKR GSM 1400 board.
I hope that clarifies but if not feel free to ask for more details.