Install ISPCP to seperate partition

[LinuxNewb]

I'm on Ubuntu 9.04 and have successfully gotten everything installed on a basic setup and will be adding a How-To since it needs updating, but I have some specific questions as to how ISPCP functions and things I want to change for my real implementation (right now I'm doing everything on my virtual rig).

I have a 1tb hard drive with a /root partition (20gbs), /boot partition, swap partition, and then 2 seperate partitions. 1 is /srv (300gb's) for ISPCP and the other partition is specifically for my media hosting. Both extra partitions are created using ext3.

I essentially want the root /var/www path to be a nice simple custom made php site I've created and then I want to install ISPCP on the 300gb partition and have Apache direct to it as an alias.

As of right now it seems like ISPCP takes control of the /var/www root path considering that anything Apache2 outputs has to be in /var/www/ispcp/gui

So I guess my question is how difficult would it be to have ISPCP run on a separate partition? Sorry if it's a noobie question. I've taught myself all my linux and considering at work all I play with is IIS/M$ Server this is a big transition