In most situations, it isn’t advisable for two operating systems to share the same partition, particularly if both are Windows OSs. For example, you can’t install Windows NT and Windows 2000 on the same partition without some potential problems cropping up. The primary cause is that both platforms share the \Program Files folder, which can lead to application problems that are hard to diagnose. Getting around this tricky issue is not impossible; it just requires a bit of hide-and-seek.

To each their own
The best solution for creating a Windows’ mulitboot system is to install the OSs into their own hidden partitions. If you didn’t hide the partitions from one another, all the operating systems you installed after the first one would be installed to the D: drive, E: drive, F: drive, and so on, but not to drive C: because the first operating system will be hosted on the C: drive. A way to get around this is with a program such as PowerQuest’s PartitionMagic, which can dynamically hide partitions. Using this type of program, install the first operating system and then hide its partition, install the next OS and then hide that partition, and so on. Each operating system will now treat its partition as the C: drive.

Using NTFS
If you want to install Windows 9x/Me and Windows 2000, you can achieve a similar result by using NTFS. Create an NTFS partition to hold Windows 2000 and a FAT32 partition to hold 9x/Me. Install Windows 2000 to the NTFS partition and, once it’s up and running, make the FAT32 partition active. Reboot and install 9x/Me to the FAT32 partition. Because that operating system doesn’t recognize NTFS partitions, it will treat its drive as the C: drive. When you need to boot Windows 2000, use Fdisk to make the NTFS partition active and then reboot.

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Check out the following TechRepublic articles for more information on multiboot systems and hard drive partitioning: