Typically this sort of question is better answered on Superduper forums, as it's their software.
I suspect Spotlight is indexing the external drive, why it's busy and can't be unmounted.
So head to System Preference Spotlight and turn off indexing except for the boot drive, also change the name of the clone as OS X gets confused if there are two drives with the same name.
If after rebooting you can't unmount the drive, try this
Drive won't "unmount". First check for Spotlight or open programs using the drive/volume, reboot.
>>>Force unmounting launch Terminal type diskutil list and press enter/return for a list of devices.
>>>Take the Identifier and add here for disks: diskutil unmountDisk force Identifier and press enter/return.