Is it advisable to run multisite from it´s own directory?

Hello,

I have to create a bilingual site. I´ve decided to take the multisite approach, creating a different site for each language and linking those two version with a plugin. I intend to use subfolders like these:

mysite.com/en
mysite.com/es

I have already created a first draft for the english version of this web (just a regular version of wordpress without multisite functions) which is working from within its own folder. I was hoping to be able to just activate multisite for that version and run index.php from the root. But I´ve read that it’s difficult to get the multisite working if it isn´t installed directly to the domain,the problem is that I can’t take down the current site on the main domain right now.

My question is: should i activate multisite functions from within the current directory? or would it be better if I create a new installation at the root directory in my host?

Thanks on advance for your help