Hi,
I want to use qmail with my domain example.ath.cx (by dynds) and with the regular system-accounts, not vpopmail.
I have written my FQDN smtp.example.ath.cx in /var/qmail/control/me, as stated in qmail-control(5).
With vpopmail, the mail was immediately sent from smtp.example.ath.cx to the virtual domain example.ath.cx, but without it, it tries to connect to a host named example.ath.cx, which does not exist, and the mail bounces.
I solved the problem by writing a line like
into /etc/hosts, where 192.168.6.2 is the mailservers's IP, but I'm sure that's a terrible hack.
Anyone having a better idea?

Looks like a simple domain problem and you seem to have found the most direct way to deal with the matter. It's not really something you need to solve in qmail.

If you're only managing a few local hosts, then yeah, /etc/hosts is the place to do it. If you need to manage local DNS information for multiple servers and subdomains, then you would probably want to create your own local DNS schema and setup a server.