Let me throw in some of my layman's knowledge.
I had the similar issue. Let's say you have two drives in Windows- C and D. D was kind of empty for me and i wanted to use that one. It was already formatted in NTFS format. So when i tried setting up Linux ( Fedora C4), it would not let me select the automatic thing, as i probably did not have any disks unformatted or in Linux required formats.
So, i selected the manual format and chose D drive (/dev/hda3) for some of the / and /root configurations, to be formatted in ext3 format. I didn't really know how to configure the /boot stuff. So after formatting in ext3 format, I stopped the installation and i restarted it again. Now, this time since D (/dev/hda3) is already formatted in ext3 type, it let me choose automatic formatting and i proceeded from there.
This is a roooundabout sick solution, but this is what i did. Someone might be able to tell you, how to configure the whole disk thing manually itself.