Any AMD64/Opteron system should be new enough that this won't be an issue, all of them should have system BIOS support for 48-bit LBA.
As far as the OS goes, make sure that you are using WinXP + SP1a, and install the "48bit LBA flush cache/hibernation" hotfix from MS too. (Should also be included in SP2, when it is released.)
Oh, WinME.. I don't think that it will support 48-bit LBA, unless you use a 3rd-party PCI IDE controller card, that shows up as SCSI in the Device Manager. (Such as a Promise Ultra100/133 TX2 card, which I personally use and would recommend.)
Any reason why you don't want to simply install the 32-bit version of WinXP in the meantime, instead of WinME?
Edit: If that is a Dell "Restore CD", and not a regular WinME installation CD, then you might not even be able to install it onto this new system. Most major OEM restore CDs are locked to the BIOS of their particular mobos, and will not install on different ones.
If you manage to get it to install, and insist on running WinME with the HD on the onboard IDE ports, then you must limit your use of the drive to the lower 127GB. (Although, if the BIOS supports 48-bit LBA, it might be possible to run in "MS-DOS Compatibility Mode" for the HDs, in order to route all disk-access calls through the BIOS. However your disk performance will take a MAJOR hit, probably between 10-20 times slower than using the normal WinME protected-mode disk access drivers. That's the reason I suggest getting a PCI IDE controller card.
Actually, does anyone know if the NVidia system drivers for Win9x/ME, will support protected-mode access to 48-bit LBA HDs? If they do, then you may be in luck. I overlooked that possibility at first.
The problem is, most normal IDE "miniport" drivers, still are accessed though the main MS IDE "port" driver ("ESDI_506.pdr"), which is where the limitation on support of 48-bit LBA lays. A 3rd-party PCI IDE controller card that shows up as a SCSI device, bypasses the IDE port/miniport driver entirely, and therefore bypasses the limitation as well. Support for 48-bit LBA in that case, is dependent on the controller card drivers alone.