My hostname is jam.luxurywebhosting.com

Right now nothing resolves or anything.... (Redhat9 Section post there)
But

My question is:

In the future I plan on adding an account with domain "luxurywebhosting.com" is this ok if I use the jam. for the hostname still???

Thanks
-Todd

Yep, should be okay.

It works, but I've been dealing with DNS issues as a result of doing this. It seems, depending on how its done, that sometimes DNS zones get combined so that the server name shows up as a subdomain in domain.com's cpanel and other times it seems seperate. How does everyone else typically set this up?

I'm curious about this myself.

Is it best practice to use a hostname of:
mybox.mydomain.com or mydomain.com

Let me paint a scenario...

-My Scenario-
domain: mydomain.com
hostname: mybox.mydomain.com
nameservers: ns1.mydomain.com, ns2.mydomain.com
zones: mybox.mydomain.com, mail, ns1.mydomain.com, ns2.mydomain.com

After just having setup those 2 private namerservers what zones should I have? WHM has created those 4 listed above. Is that normal? What should each contain?

I gather that my next step would be to create an account within WHM for myself using my domain of 'mydomain.com'. Is this correct?

Any help would be appreciated.

box.domain.tld is usually best, that way you can still use the actual domain for other things aswell.

I have:
domain: domain.com
host: box.domain.com
NS: dns1.domain.com dns2.domain.com dns3.domain.com
zones: domain.com, mail, dns1.domain.com, dns2.domain.com, dns3.domain.com

Originally WHM setup a zone for box.domain.com but it kept causing errors and box.domain.com wouldn't resolve, so I removed it and everything has worked fine since.

Yes

I gather that you then setup the zone domain.com by yourself or did WHM set it up? I seem to be able to resolve mybox.mydomain.com. When I setup my account for 'mydomain.com' won't that create the dns zone for mydomain.com or is that somehow slightly different?

sorry, that was added automatically when I created the account for domain.com

Cool. Sounds like I maybe up to creating the account. I'm slowly getting there. Thanks for sharing.