Payment Method in WooCommerce Advanced lets you group Payments created from incoming WooCommerce Orders so they are easy to see, sort, and select as a group in the Deposit tool.
Big Business users who enable WooCommerce Connect have usually been entering manually and already have a Payment Method associated with WooCommerce for this purpose, so it is simply a matter of selecting in the WooCommcerce Settings to have automated entries match.
Note that mapping to Payment Method in your WooCommerce Mapping will overwrite this.