I'm trying to do the same thing. I got my subdomain working, but now my regular domain doesn't work.
I have mydomain.biz registered with godaddy. It's NS entries are ns1.afraid.org and ns2.afraid.org. Here's what I did.
1) Added secondary NS on afraid.org to ns1.dreamhost.com and for ns2 and ns3.
2) Made an NS record on afraid.org for d.mydomain.biz to ns1.dreamhost.com (not sure if this is correct...)
3) Tried to add mydomain.biz from the DH control panel. It wouldn't let me.
4) Added ns1.dreamhost.com to the nameservers at godaddy.
5) Added mydomain.biz to the DH control panel and removed hosting.
6) Added d.mydomain.biz to the DH control panel.
7) Clicked on DNS for d.mydomain.biz and got the IP address for the A record.
8) Added the A record to the IP for d.mydomain.biz at afraid.org
Immediately d.mydomain.biz started working and mydomain.biz was still working. After a while mydomain.biz stopped working but d.mydomain.biz is still working.
I tried removing ns1.dreamhost.com from godaddy and it's still in the same situation. Not sure DNS has propagated yet. Should I have removed that, or is that going to break d.mydomain.biz too? Any ideas how I can get mydomain.biz working again?
Edit: Now mydomain.biz is working. The only thing I changed was removing ns1.dreamhost.com from godaddy. Now I'm not sure if d.mydomain.biz will be working for much longer.