If your Time Machine hard drive capacity is high enough, Time Machine can back up your external drive. It's just that external drives are excluded by default. You can include the drive by going to Time Machine Preferences -> Options. In the "Exclude these items from backup" list, remove your external drive. This also applies to DMGs and Sparseimages that you may be using.
Having said that, I don't think its possible to use two separate Time Machine drives to back up your internal and external drives separately (i.e. internal to drive A, and external to drive B).
Edit
SuperDuper! or Carbon Copy Cloner are other excellent options for this, if you don't need the incremental backup plan that Time Machine provides. The pay version of SuperDuper allows for Smart Updates, which only transfers the changed files. Carbon Copy Cloner also does this, using rsync as the underlying transfer method.
I use SuperDuper! every night to make a bootable backup of my internal drive, and have also used it to clone external drives as you wish to do.