My question is about the climate control scheduling on the My Skoda app. Actually to be precise, I am a bit worried about what battery it uses to use the climate control / air conditioning. As we have pretty cold mornings over here (-25C even) I'd like to preheat the car before entering it. I have the subscription for it.

But once for whatever reason, the 12 volt battery went flat, so I just want to make sure

Does it use the 400 volt drive battery or the flimsy 12 volt that is under the back seat while running the air condition on program?

The heating (PTC element) or the cooling (electric compressor) are both powered from the HV battery. The "brains" of the process, control and coms with the servers (if you send the command from the App), power relays and (I assume) the cabin ventilator (that blows the heat or cold inside) are fed from the 12V - the flimsy as you call it.
If you have the car connected to a charger (HV) before you leave, ideally you should charge the last 10-20% of the HV battery before you leave - this also acts as some sort of pre-conditioning of the battery, since it raises a bit the temperature while charging (you mentioned very cold weather). In this scenario, starting the cabin heating several minutes before you leave should have no impact on the 12V battery, since the VAG logic is to also charge the 12V battery (if needed) while charging the HV one.

p.s. looking at the screenshot you sent, I realized I miss the exterior temperature showing in the Skoda App. The idiotic Cupra App doesn't have that displayed, and I bet the information is available on the server (sent by the vehicle when requested)

Edited 31 October, 202531 Oct by SkOmk4

18 minutes ago, SkOmk4 said:

p.s. looking at the screenshot you sent, I realized I miss the exterior temperature showing in the Skoda App. The idiotic Cupra App doesn't have that displayed, and I bet the information is available on the server (sent by the vehicle when requested)

They removed it from Skoda app as well for about 2 years for no reason. Reappeared very recently and was announced as a new feature lol.