I am research your same conflict. I have a T41, and it also has the IBM Predesktop Area on it. Since mine did not come with any recovery cds I want to do it right the first time. Here is a good link
for other people that have had success. Let me know if/how you got a good dual boot going.
I have tried partition magic (pm), I went through the wizard in windows to resize and set up my partition, but upon reboot I get and Error 27: Cannot Lock Drive from pm. But as far as pm seeing the predesktop area, it does not. If you go into the bios and set the predesktop area to disable, and then boot into windows and take a look at pm, then you will see the predesktop area is about 3GB. The default setting is normal, which allows you to partition the drive, but hide the predesktop area from being touched. I have a 60Gb drive so pm sees it as a 57GB (roughtly). My predesktop area begins at sector 110,160,... (roughly) and when I attempted to repartition/resize the drive pm make my second partition end at sector 110,160,... So it should work, but I keep getting Error 27. If I can get past that, then I am golden. I hope I made everything clear, I am rushing to go to lunch.