To which domain should I install multi-site.

I am on the first step of "Network Setup" for multisite where it tells me what my server address will be (jonhaines.com) and above that in "sub domain install" it says: "Because your install is not new, the sites in your WordPress network must use sub-domains. The main site in a sub-directory install will need to use a modified permalink structure, potentially breaking existing links."

jonhaines.com is the primary domain on bluehost and on it I have scholasticonnection.com as an add-on domain. Scholasticonnection is the site that will be using multisite (I want to allow users to create their own sites/blogs through this SC.com....which are not sub-domains, but rather subfolders (ie. SC.com/bobdude).).

Should I proceed with the current configuration? Can an addon domain be used for multisite? Does the above warning about subdomains apply to sites that I will be creating under SC.com? What should I do and how should I make those changes if any?