Doogee I wouldn't recommend installing windows (no capital) after Linux if its 2000 or Xp. The aforementioned will, in my experience (well, I've only tried it with Xp but I've read its the same with 2000) f*ck around with your Linux partition, more so if its ext3. Not just the bootloader, it will corrupt the partition and it is very hard to recover the partition and its data. If its 9x/me fire ahead with your installation, it'll just overwrite the boot sector to load windows only; so make a bootdisk and install LILO/Grub.
Either way be very careful about partitioning. Do not under any circumstance use DOS FDISK, parted or GNU's fdisk is probably the best option.
BTW, I know what its like, you do or will need that windows installation for something. For me I need it for those devices inaccessible in Linux because of the manufacturers won't release drivers (on my system, that's just a scanner)... so I won't nag you about installing windows.