Windows 98 issues: Upgrades
1. When you have a great many installed
The best possible way to install Win2000 on a Windows 9x system is to create a parallel install. This means placing Win2000 and Windows 9x in separate directories or separate drive partitions. This isn't hard to do and is spelled out later in the installation instructions: all you need to do is specify a different directory than the existing one for Windows. But be advised, you must have at least 850 megs of free space on the target drive to do this. To be on the safe side, we recommend at least a gig free. (See our Resources section in the Pre-install Checklist for the lowdown on system requirements.)
For best results with parallel installs, use another drive. One reason for this is that Windows places components in the Program Files folder of the system drive that may not be cross compatible with other Windows versions. If you have Win9x on C: and space on D:, install Win2000 on D:. This way you'll have two discrete Program Files directories, one on C: for Win9x and one on D: for Win2000. No possible confusion there. Trust us in this, putting Windows versions in their own partitions is the most reliable way to work with a multiple-boot environment.
Windows 98 issues: File systems
On the other hand, if you're looking for the best mix of interoperability and security, use FAT32 as a happy medium between the OSes. You can use a FAT32 drive as a data repository while you upgrade your OS and application drive(s), then convert the FAT32 drive to NTFS using the Win2000 command line command:
Down the road, though, think about moving any data you need to migrate between OSes completely offline
Windows NT 4.0 issues: Upgrades
Despite this, it's best not to chance anything. Stick with doing a good, thorough set of backups before you upgrade. This includes everything
Remember, your best operating system installation is always a clean installation, where no previous operating system was upgraded.
Windows NT 4.0 issues: File systems
Also bear in mind that Win2000 will upgrade the NT Boot Loader to a 5.0 revision. That alone doesn't create problems, but some people notice it and are worried about it. It is, however, completely backwards compatible.
Unlike Windows NT 4.0, Win2000 is designed to upgrade a PC running Windows 98 or 95. Based on our experiences with such upgrades, though, you'll get far cleaner, faster, and more dependable results if you avoid upgrading an existing Windows 9x setup and simply start clean.
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2. When you have many user accounts or settings that cannot be readily migrated.
Still, the best thing to do is to employ everything in your power not to upgrade an existing installation. We've had far too many bad upgrade experiences with Windows 98 (and Windows 95) machines that were irretrievably trashed as a result of the upgrade. (Besides, it's always best to avoid operating system upgrades where possible.) If you're determined to upgrade instead of clean install, please do the smart thing and back up everything before proceeding, both data and system files. Don't kid yourself into thinking you're exempt from disaster.
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If you're upgrading from Win9x to Win2000 and you can afford to reinstall your apps, your best bet is to start with a clean slate.
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If you're installing Win2000 on a Windows 9x system, you need to think about the file-system issue -- even if you're upgrading Win9x. Win2000 works transparently with FAT (also known as FAT16) and FAT32, which makes it possible for Win2000 to coexist on the same drive as a Win9x installation, without any major problems.
Even so, no version of FAT should be left on the system if you want take advantage of NTFS security features, and any Win2000 installation on a FAT or FAT32 partition will be far more vulnerable to casual attacks (all someone has to do is put in a Windows boot floppy to get into the system!) than if the system were on NTFS drives.

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Although Win2000 works with FAT and FAT32 drives, it can't support advanced volume features like security descriptors under FAT.
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CONVERT {drive letter}: /FS:NTFS
Upgrading an NT 4.0 system to Win2000 has in our experience gone far more smoothly and with fewer complications than any Win98-to-2000 upgrade. This is probably due to the close brotherhood under the skin between the two operating systems: they have a lot in common.
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If you plan to mix NT 4.0 with Win2000 in a multi-boot environment, beware: Win2000 upgrades all NTFS volumes, making it impossible to run NT 4.0's CHKDSK on them.
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If you're mixing Win2000 and NT 4.0 on one PC
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