The EFI System partition is not normally used by Mac OS, although some boot loaders use it. (IIRC, Boot Think puts its stuff there, but I don't know about others.)

I recommend you do four things:

• Use any reliable OS X backup tool to copy the disk's contents to your new disk (either directly or indirectly). I've used Carbon Copy Cloner for this task with good results. This will back up your system, but the resulting disk will not be bootable.
• If you're concerned about the EFI System partition, mount it manually. You can do this in OS X with the "mount" command, but you'll need to know the partition number and you'll need a mount point (an empty directory) handy. Something like "mount /dev/disk0s1 /mount/point" should do the trick. If there are files there, copy them manually. (You can mount the EFI System partition on the new disk in a similar way.)
• Prepare an emergency boot disc. Something like Empire EFI will probably work fine. The idea is to be able to boot your copied OS using the boot loader on the emergency disc rather than your regular boot loader. You can test this with your current disk before you do anything. After copying your files, boot the new disk with your emergency boot disc.
• With the new system booted, re-install your boot loader. Track it down on your original installation medium or on the Web and follow whatever procedure it offers to install it. This may be an automated installer or a set of commands typed in a Terminal screen.

There are other ways to go about this, but this one's pretty flexible, and if something goes wrong, you should at least be able to boot your old system to get on the Web and figure out how to work around the problem.