Command Line method to backup using two Time Machine disks
Note: The restore component of backing up like this has not yet been tested.
Get the ID of the attached drive
defaults read /Library/Preferences/com.apple.TimeMachine BackupAlias                       

Eject, plug in 2nd drive, make it the Time Machine drive with the GUI, repeat.
Write (rather than read) the ID:
defaults write /Library/Preferences/com.apple.TimeMachine BackupAlias '&lt;00000000 014e0002 ....&gt;'                                                   

source &amp; thanks to Christian Stocker. Key comments from that post:

http://developer.apple.com/DOCUMENTATION/Darwin/Reference/ManPages/man1/defaults.1.html &quot;WARNING: The defaults command will be changed in an upcoming major release to only operate on preferences domains. General plist manipulation utilities will be folded into a different command-line program.&quot;

Also the property DestinationVolumeUUID should be set.