Multisite, SSL certificates, and eCommerce


Anyone running a multisite network handling eCommerce?
How are you handling the SSL certificates?
I bought a multi domain SSL certificate and used the first 3 SANs that came with it to protect two of my customers. I thought I just logged in to WHM and installed the certificate and that was it, but it turns out that no. Here's where things get tricky for me.

I was told by my web host that I need to create a new account in WHM for cPanel using my client's domain and then install the certificate under that account. Fine, I went ahead and created the account.

I went back to the registrar and changed the name servers of my client’s domain to match the ones from my server, but now all I get is

You don't have permission to access / on this server.

Additionally, a 403 Forbidden error was encountered while trying to use an ErrorDocument to handle the request.

I can’t see the website. How are you guys with a Wordpress eCommerce network handling this to make it all work. Is there a way to have all the domains and certificates under one cPanel account so I can install the respective domain certificates in there?