New MU Super Admin requests advice and suggestions

Back story: I do web design and hosting. I am also a huge Genealogy buff. I use The Next Generation of Genealogy Software (TNG) with a plugin that integrates it with WordPress. There is a growing community of TNG users who have integrated with WordPress and some would like to see the development of some kind of network or community.

I recognized a singular opportunity to use my business site to create a multisite network that would include the opportunity to sign up for a hosting account.

I have the network set up and functioning but I'm still fumbling around a bit. I think I need to create a mu-plugins folder for some plugins, but am unsure which should be there and which should be public.

Any advice and suggestions that would aid me in optimizing my network would be greatly appreciated! I am rather anal about security so any suggestions along those lines would be greatly appreciated!

Thank you!!