Installing a seciond instance of Wrodpress in a subdirectory

Hi! So I would like to run a different template for a course area on my site. So what I am thinking of doing is setting up Multisite. My question is - will Membermouse still have full functionality inside of the subdirectory? That is to say, can I have Membermouse running on the main site and it having control over the Multisite contents?

I hope I am making sense here.

Thanks for any help :)


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