How to work with CourspressPro and Multisite

Hi, how can I get the menu links of coursepresspro out of my front page menu structure on my main multisite landing page and into its subsite? I'm working with multisite and created courspress pro as a sub directory site on my divi powered main site like this http://thummimng.com/course but once I network activated courspresspro plugin, the menu links jumped into the main site menu structure and also the sub directory site shows of coursepress shows paga not found when the site is viisted hence how can you help solve this? Also, does CoursepressPro compatible with WordPress multisite because its one of the main reason to activating multisite.

And this is how it was previouslyl screenshot link: http://awesomescreenshot.com/0fb457pg5b