If you are using an installation of Windows on one of the two partitions that requires Asian or non-Western language...
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support, be sure to install that last as it uses special extensions within the boot loader to provide proper display support for the boot menu. Since in both cases you are installing Windows 2000, the second installation of Win2k should detect the presence of the first and incorporate it into its own boot menu.
Whenever you install multiple copies of Windows 2000 on a system, the boot loader is overwritten with the most recent version for the last OS to be installed on that system. The choice of file system is up to you, unless you have specific reasons to use FAT32 -- for instance, for backwards compatibility with other OSes.
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