Everything seemed to go fine with the installation of both CoursePress Pro and the bundled MarketPress plugins. Fantastic plugin, saving me TONS of extra work!
I ran into the problem that once I entered all the Payment Gateway data I could not click the Save Changes button. I don't mean it was grayed out, I mean that it was visible but did not appear to be a button.
Thankfully, I did find both the problem and a temporary workaround.
Bug caused by Footer Content from the WPMUdev Branding plugin. It seems to have created an overlay over the button.
Obviously, just disabling the Footer Content is not the solution I am looking for, as I am using the Footer Content for a reason. As a temporary solution I noticed that simply checking any one of the payment gateways I am not using also Saves Changes. So every time I needed to change something I checked, then unchecked a option I was not interested in.
My workaround is fine for me, but I am about to launch my Multisite for less techy people, and this isn't really going to work for them, so please fix the bug!