How can I register a user to a WooCommerce site that did not checkout?

If I want to add a user who has not gone through the woo commerce purchase process, I can add them as a WordPress user. To then assign a course to that user, what is the best way? To use the "edit courses" button and then click on "register user" next to the course name? Or can I "edit invitations" and click on the + and add a new invitation with multiple courses and or users? Can i edit existing invitations to add either users or courses?

So yes, you can create a registrations for one or more learners to one or more courses in this way [either way actually].

Yes you can edit existing invitations. But for a license key invitation, adding a course will require you to edit the JSON metadata field as this is where the seats available data is stored.