Advice on WP-MultiSite and CloudFlare

I'm using a WP-Multisite install on one of my shared hosting PBNs. Here's what the setup is approximately like:

www.primarysite.com - this is the WPMU install
www.primarysite.com/subsite1
www.primarysite.com/subsite2
www.primarysite.com/subsite3
etc - these are the multisites made using subdirectory method.

I then added the following domains as ALIASES (ie parked domains) to the hosting plan:
subsite1.com
subsite2.com
subsite3.com
and then domain mapped them to each of the subdirectory sites...
www.primarysite.com/subsite1 mapped to subsite1.com
www.primarysite.com/subsite2 mapped to subsite2.com
www.primarysite.com/subsite3 mapped to subsite3.com

Now, I want to shift primarysite.com as well as all the domain mapped sites to a cloudflare account. How would I go about doing this?

(this is specifically a question for WPMultisite users, it won't make much sense for someone who hasn't used multisite)

Bump.