I'm needing help with this too. Right now I have 2 courses, each have their own member area. To: Ash97, you can only have up to 10 courses on your site which means 10 member areas.
My struggle is that I want people to be able to have the option to buy both courses. Like add both to a cart and checkout at the same time. But having to join 2 different member areas makes no sense.