Maybe I'm missing something, but I don't quite understand what you're asking, or how it links to a unique IP. You probably won't need a unique IP unless you need an SSL cert.
You don't lose control of a domain by transferring it here, nor do you have to transfer it here to host it here.
All domains and subdomains get their own folders. There's no connection to having a unique IP there.
If you're unsure of anything, I'd recommend picking a new domain with the free domain you get when you sign up. That way, you can get it setup and see how everything works, so you'll be familiar with the panel and everything else.
Then you can setup your other domain here, since all plans host unlimited domains. Once you have it setup, all you have to do is log into where you registered your domain and point the nameservers to ns1.dreamhost.com, ns2.dreamhost.com and ns3.dreamhost.com.
See this Wiki article for testing a domain here before switching the nameservers over: http://wiki.dreamhost.com/index.php/DNS_-_Viewing_site_before_DNS_change
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