Most of the guides are set up to run it as WMware. IIRC, WMware allows you to run another OS concurrently with the one you booting into, as a virtual machine. I.e. You boot into windows, and you run OSX in a window.
I think if you want to run it directly, you need a blank separate HD. Most how to guides suggest this. Might be to do with how it handles boot sectors/master boot record and such, don't forget, you aren't supposed to do this, OSX was never designed for it, it was design for Apple x86 hardware only.
