You need to install XP/2000 on

Different partitions.
You need to install 2000 first, then XP. If you install 2000 later, it will replace the XP version, and it will failed to load. And give you the NDLDR missing error.

Copying these to floppy is not right, you should boot into c:.

You can try this, try to install XP again, but after it copied file and reboot first time (before text mode installation), stop the install, and boot into Windows 2000, then remove the entry in BOOT.INI. Usually is the last entry that point to the installation folder. Then try reboot. It might be able to boot.

Make sure you install different versions into different partitions.

Have not played with Partition Magic, don't its role in this problem.