There are no specific exploit pôssible if you run multiple instances of apache on different ports. HOWEVER, you should NOT run apache as root (for a cp for example) as if one manage to exploit it, he just broke into your system.
To set a virtual name server, I assume that your ISP already has a NS for you and you want to use it under your name. If that is the case, simply register your domain as being a name server using the 2 (or more) IPs of your ISP's NS.
For example, if your ISP's NS are:
The name server you would register would be:
However, anyone doing a reverse IP lookup will get your ISP's name and not your. If you want your name, you must ask your ISP to allocate you 2 dedicated IP on that name server (exactly how would work name based web hosting and dedicated ip based)
Is that clear?