Windows will overwrite your master boot record. You can't stop it from doing this. After it overwrites your mbr, you can't access anything but Windows.
But with a bit of preparation you can protect yourself. The easiest way is to use the dd command in linux to make a backup of your mbr.
Thus, if your boot drive is hda, you enter this line:
dd if=/dev/hda of=~/bootblockbackup.bin bs=512 count=1
This will copy your mbr to a file called bootblockbackup.bin in your home directory.
Now install windows.
Then, use a Linux boot floppy, or a live CD to start Linux. Go to your home directory and type in this command:
dd if=bootblockbackup.sh of=/dev/hda
This will rewrite your bootblock to the way it was before. Now your problem is that you won't be able to access Windows.
If you are using lilo, I don't know how you fix that. I use grub and in grub you would go to your /boot/grub directory and add lines like this to the file menu.lst:
Code:
title Windows
root (hd0,0)
chainloader +1
These lines assume that your Windows is on drive 0 (hda) partition 0 (hda1). If Windows is someplace else, modify the root line accordingly.