I'm almost completing an online service where people can link their domain to. Think Squarespace/Wix/Weebly type. Visitors enter customerdomain.com that leads to mywebapp.com but keeps customerdomain.com/page in the addressbar and forward that to mywebapp.com/page. There is only one leading domain, content is technically accessible through both domains. Sites are dynamically identified by the domain name and generated without frames.

Currently I'm using a Alias Pointer and using the canonical tag pointing to customerdomain.com for SEO, and this technically works fine..

But I'd like to allow for SSL, subdomains, email hosting for each domain and keep in mind that my client or I will own the domain(s). Ultimately I'd like to automate adding domain names within the webapp by my customers.

How will this affect my (customers') SEO serving hundreds of sites through 'one' webapp? is Canonical enough? Other technical setup? More IP adresses? How much per IP?