Well, the simplest/preferred way to do that is to do what you suggested as your second though – just create a Sub Server under your main domain for junk.domain.com.
That is, select domain.com from the drop-down on the top-left, click Create Virtual Server, choose Sub-Server, then enter “junk.domain.com” as the Sub Server’s domain name.
Yep, what Eric said. A sub-server is the easiest and recommended way.
It’s also possible to configure this manually, without a sub-server, but then you’d need to manually edit the BIND zone and use Apache’s mod_rewrite, which is “not for the faint-hearted” as Dumbledore would put it.