If you are truly cloning the drive using something like Acronis True Image or Norton Ghost, you should not need to make this decision.  A clone is just what it says; a complete duplicate of the original drive.  The only difference should be the result of using a larger drive than the one you're cloning.  Cloning software generally increases the size of the partitions proportionately so that the drive is filled.  The FAT 16 partition holds the Dell diagnostics and gets nothing added to it, so you should be able to set a parameter that tells the cloning software to keep it the same size as it was on the original drive so that all the additional space gets assigned to the NTFS partition - your C: drive.

You don't need to worry about the MBR; it always goes to the same sectors on every disk, right at the beginning.