When I first get into the car, if I spend time messing around with the nav/settings etc I get a warning message on the screen to the effect that the battery is low and to switch on the engine otherwise the screen will turn off automatically! Is it referring to the main vehicle battery? Does it mean my brand new 100a battery really is low?

 

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Your car just told you your battery is low.
"Some Time" messing around... over a few minutes will do that every time. There are a LOT of modules running, even with just a door open.
The best advice would be to fully CHARGE your battery using an actual battery charger. Not a maintainer, not a trickle charger. Then don't use the electronics without the engine running for more than a minute.

 

Yes, the main battery. That is exactly what it means, and if you do not recharge the battery (fully) you are likely to get different warning lights or malfunctions showing up. Full battery voltage is crucial for these cars (and all modern module-laden cars).