CQ mapping and apache configuration for multidomain

I want advise on best approach for implementing the URLs mapping for multidomain site in CQ5.5

Here is the case:

I have around 600 websites that has to be maintained in CQ. It is fine. Now i have to maintain 600 domains for each site.

Apart from CQ, I have other ATG server that maintains other data/services. We have to use single domain for serving CQ as well as ATG.

We are planning to add a identifier in URL for distinguishing between CQ and ATG url (content/website/en/cq/homepage.html ), but it seems it is not seo friendly. Is this is the right approach to control url redirection ?

What is the best way to store the domain mappign for all the site- sling mapping or at apache layer?

Please advice on CQ mapping and apache configuration.

Thanks