hi @tehcook
yes you are right, it was not yet ready with the documentation but we now catched up with that and you can find the installation instructions for V2 on the official docs here https://docs.btcpayserver.org/WooCommerce/
The difference to the old plugin is that it was based on the BitPay API which has had its limits. The V2 is based on the new Greenfield API that allows a lot new features like refunds. Currently V2 is on feature parity with the old version but has a more modern architecture and also allows much easier separation of payment gateways, e.g. you can have separate gateways for BTC and LN and with some other 3rd party modules this allows you to e.g. give discount for LN payments.
We decided to do it in a new plugin as it is a complete rewrite and an automatic upgrade would break the plugin as the old plugin uses the BitPay based pairing while V2 used API keys with permissions.