In requesting a PTR record setup from TP, I asked for two entries for my "main" IP address, one for domain.com and one for ns1.domain.com. I guess you can only have one entry for each IP though...so I am not sure if my root domain or my primary nameserver should be listed on the R-Lookup...what do you guys think?

Yes, you can only have one rDNS entry per IP address. You ought to set it to the hostname of the server.

We just leave ours to the default rdns records so that we're invisible for any resellers on that ip. This way the ip can be traced back to theplanet, but not our company or our resellers directly and we can save ip's by allowing more people to share them.

Also, I was told by the aol postmaster that mail should still get through to them as long as something is in rdns, including the default theplanet rdns and that I didn't need to use my domain in rdns.

So the entry should point to the (FQDN) hostname, or the short version of it?

my (FQDN) hostname = server2.domain.com
my "master" domain = domain.com

That brings up another question. I have my hostname set as server2.domain.com right now, as the setup said it had to be fully-qualified. Now I have server2 showing up as a subdomain on my "master" domain's account. Should it be like that? I used CPanel several years ago and do not remembering it adding a sub-domain for the hostname like that.

Any ideas?