Doesn’t that depend on how you want to use the nRF9151 feather?
e.g. if you want to run it from battery, then use GND/VBAT. If you want to power it from USB, then use GND/VUSB.
The 3.3V is AFAIK an output, means you may use it to power some external devices (with care not to drain the battery). If you want to connect the PPK II here to measure the external devices, then you need to connect 3.3V ( output) to VIN (PPK II) and VOUT (PPK II) to those external device. You will then only measure their consumption.