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Windows ME doesn't appear to have any way to load more than one os like 98,2k, & xp. You will either have to install the Linux bootloader to the windows hard drive (not partition, see below), or bot linux from a floppy.
If you choose to install the bootloader to the windows drive, no partitions will be created. The hard disk's MBR is where the bootloader will be placed. You can restore the Windows MBR with the rescue floppy (see control panel->add/remove software). From the DOS floppy, run 'fdisk /mbr' and the Windows MBR will be restored.
The install program will do the work of partitioning the second hard drive for you.
Linux has no problem installing the boot loader on a fat partition. (/dev/hda) There are two loaders you could use, lilo and grub. If you go with what the installer says, you will be fine. When you are done, there will be a multiboot menu when you start, and you can start up either windows or linux from there.
Be sure that you make a Windows ME rescue disk. It will allow you boot up and run 'fdisk /mbr' if for some reason you need restore the original windows MBR.
By the way, in linux the second hard drive is called /hdb for an IDE drive. The first partition is called /hdb1, the second regular partition is called /hda2. If you have an extended partition, it is /hdb4, even if you don't have other regular partiitons. The partitions contained in the extended partition start at /hdb5.
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