Subdirectory Fresh Install – Multisite Network Question

I’ve been using WordPress for a while now on a number of sites, but this is the first time I’ve tried setting up Multisite and I’m a little confused about one aspect of it. Hoping someone can clear this up for me.

I have a main site that has been running for years. Let’s call this mysite.com

I’ve done a new install of WordPress in a SubDirectory of that site because I do not want to to be found at mysite.com. So it is currently located at mysite.com/blogs

I go into Tools > Network Setup to start setting up for multisite and here’s where I’m confused.

Sub-directory Install Because your install is in a directory, the sites in your WordPress network must use sub-directories.

Server Address The internet address of your network will be mysite.com.

Does this mean that my Super Admin area has to be located at mysite.com or can it still be in mysite.com/blogs with each site located at mysite.com/blogs/1, mysite.com/blogs/2, etc. or is it necessary to have my main wordpress installed at mysite.com? I don’t want it there because I already have a regular website at that location. I may simply not be understanding the whole setting up a network thing because it’s new to me, but I hesitate to click install in case my main wordpress site ends up in the wrong place. Hope this makes sense!

Any advice would be greatly appreciated! 🙂