Google-apps – Is it possible to add additional paid users to a Google apps for business account whilst keeping the existing free users free

It really depends on what kind of services you want enabled on the respective domains and what you need for each of them.

If you have 10 domains under your control, but 7 of them were registered to catch those spelling mistakes in accessing your main domain, then it would be good to add these 7 domains as an alias to your main domain in Google Apps.

As for the remaining 3 domains, lets say they were registered as special domain names for the different projects in your organization and not everyone in your organization is involved in that special project. If you don't require Google Sites for that domain, then you can just add the domain as another domain within your parent organization's Google Apps.

Like you said, adding all the domains into one Google Apps is good as it is a central area to control things, though it is subject to certain limitations. You should have a separate Google Apps if you want to enjoy all the benefits that a primary domain has, for that special domain name that you might have.

As you already read from the Google support pages:

at this time you can't change which domain is your primary domain.

You can't do it. So there is no way of "keeping" your free Google apps plan if you insist on changing the primary domain. However, keeping the primary domain is not usually a problem if all you want to do is change the "Organization name". You can change the Organization name under Domain Settings -> General. Once you add the new domain name to the account you can also log in at google.com/a/newdomainname.com.