Some files and directories can't be moved at the moment:
antivir ==> AVIRA expext this dir in the root (I doubt it will work from PXE, unless you modify the initrd)
/boot ==> ISOLINUX/SYSLINUX expect that there config file is in /, /isolinux (/syslinux) or /boot/isolinux (/boot/syslinux). GRUB4DOS expects is menu.lst in /, /boot/grub or /grub (not sure about the latter).
/pmagic could be moved to /ubcd but then an extra parameter must be passed to all entries in the config file of Parted Magic. You will need the PXE version of Parted Magic anyway.
EDIT/ADD: As I haven't found any way to for example load new pxelinux.0 with diffirent rootfolder that would work around this issue too...
You need Syslinux 4.02 for that (you need to update all modules too (you won't find my econfig.c32 module, but you currently need to edit the config files anyway).
You can use the following:
The APPEND line will specify the new root dir.
For UBCD5.1, Syslinux 4.xx is planned to be used. It allows using relative paths and setting other root dirs, so it will make it much easier. I already though about a PXE version of UBCD, but never really started.
Download Ultimate Boot CD v5.0
Use Parted Magic
for handling all partitioning task: http://partedmagic.com/