The description for Wake On LAN says this:
Select whether to enable Wake on LAN, and/or which Startup Sequence to use after a Wake on LAN event.
This item controls the wake up event from onboard LAN and PCI LAN.
The difference between Primary and Automatic is which Startup Sequence it will use when you wake it via LAN.
As you can see in the following screenshot, these are the options Wake on LAN option will choose from depending on what you select.
Take note of the difference between the Help Message for the Primary Boot and Automatic Boot Sequences.
To answer your question of which on do you use? You can use either, as long as they are configured to boot from your desired device.
Useful resource for anyone else looking for answers on this product: TeamViewer 9 Wake on LAN Manual