There are no settings within Spybot to scan an external drive and it is not normally necessary. Unlike anti-virus programs and some other anti-spyware programs, Spybot does not do an in-depth scan of every file on the primary drive. For a brief description of how Spybot scans see:
There is a special scan for Spyware installers (files not installed yet) that can be limited to specific directories (actually it should be limited) which can be located on either internal or external drives. To activate this feature go into Spybot > Mode > Advanced mode > Settings > Directories and add directories. There is more on what this feature scans for here:
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