Installing Windows manually
What you need is the refit tool.  Then on the Mac (via DiskUtil) shrink/resize your Mac partition and create a partition for Windows in the free space. 

Then, via Refit (on the Refit boot menu under tools), sync the Mac partition table and MBR-partitions (this will create a windows-readable MBR type partition map that matches the partitions you created on the Mac).

Then just boot from a Windows CD and install in the new partition.  Do NOT modify the partitions (adding, removing, etc.) from Windows though.