Clonezilla will copy EVERYTHING on the drive to the new drive.
I use clonezilla to create clones of windows 7 64bit operating systems...
just remember that windows7 will not "See" both clone and original if they are connected to the computer at the same time (this results in something called a "signature collision")
Clonezilla will even copy the unlettered "System reserved" 100mb partition that if often created in a windows 7 installation.
Clonezilla also natively recognizes USB/Firewire/eSATA connected drives
I have never used it outside of "beginner mode" and copying "directly from disc-to-disc"
And when it asks "do you want to copy the BOOTLDR" you say YES.