I'm not sure about windows needing the first 1024 sectors. The requirement for linux needing to have the kernel in the first 1k sectors went away a while ago.
If you've got a spare drive, install the one you want windows on as the only drive and as primary master. Install Windows. Shutdown, move the Windows hard drive to be the seconary master, and install the drive you'll be putting linux on as the new primary master.
Install linux, and it should pick up the Windows drive and configure LILO or Grub to let you boot from it.
Should you want to move your linux install to another box, simply remove that drive and move it. linux about 99.9% of the time will just reconfigure automagically (or with a small amount of help from you) to the new hardware and go. Plus, the Windows harddrive has only windows and windows boot sectors, nothing from linux left over.