Wordpress Multisite SSL Question

I just turned an old wordpress website into a multisite. However, I've been presented with the following error:

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.

The thing is that I just installed SSL on my main domain and I did an Alpha Standard SSL for sub directories because I just got WHMCS .

I'm wondering if I choose Sub domains as my multisite structure if this will be a problem. Please let me know your thoughts.

My goal is to offer hosting and training...

- Jerone