Multisite on specified subdomains

Hello everyone 🙂
I have some concerns about changing my WP website into a multisite for easy management. Here’s the scenario:

I have a WP site up and running and I’d like to add an ecommerce to it.
I tried different plugins, but some of them create pages upon installation, mess up the website menus and such. So I’m thinking about going multisite and setup the ecommerce in a subdomain like store.mywebsite.com
This way I could keep some global management, let the main website alone and tweak with the online store until it’s ready.

Problem is: I have WP intalled in /public_html/ folder to manage the main site, so if I set up wildcard domains in cpanel this will affect ANY other cms that may come in the future.

Is there a way to set up a WordPress network only for a specific subdomain/sub-blog?
I could use sub-directories, but I don’t want to tamper with the /blogs/ thing… plus this could alter the main website’s permalinks.

I searched the forum but I found nothing similar to this situation.
Do you have any suggestion about this? ^__^
Thanks!