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So if I have 3.3V from my regulator, where should I connect it? Battery, external or 3.3V?

The battery pin and the 3.3 V pin are the same. That is where you connect your 3.3 V supply. No voltage will appear on the 5 V or the V ext pins.

One thing you might want to consider is this: what happens if you connect USB (to flash, to experiment) and your external 3.3 V at the same time, but your external 3.3 V is not turned on. The USB will power to the Z-Uno regulator, the diode on the Z-Uno will pass on current so about 3.1 V appears on its 3.3 V pin and that connects to your regulator. So your Z-Uno is feeding your regulator, so it is "the other way around". Normally, this should not be a big problem, but suppose you have another load connected to your external circuitry, that might overload your Z-Uno. I would either verify your design to make sure this does not happen or I'd put a Schottky diode between your external 3.3 regulator and the Z-Uno, so it never back-feeds. Or remove R12, but then you cannot flash your Z-Uno without 3.3 V supply. I do not want to underestimate your soldering skills, but you might find removing R12 a bit fiddly.

I'm looking for OTA updates (sketch) so there is no need to connect USB in normal operation. I would have to diconnect it from the battery anyway due to reachability. Thanks for pointing that out.