It's really pretty easy so I won't try to go into all the details here. Just post if you have any particular difficulties.
I assume that your reason for the two drives is to rotate them off-site. The simplest way to set up them up is to format them identically. This way whichever one is plugged in will be recognized as the backup drive and you won't be constrained to a rigid schedule. In other words, if you forget to bring the drive in to swap on the usual day, the backup will proceed as usual without any errors or intervention.
My rule about backups is to keep them simple and don't try to prepare for any possible catastrophe.
But, if you want extreme data safety, an archival backup to CDs and/or DVDs (Retrospect can mix them in the same backup set AFAIK) can be taken off-site to a third location (like a bank vault.
For the ultimate in safety and convenience you can set up dual optical drives for archival backup. This way you have one to take away and one to keep handy for easy restoration of recent files (it's a pain to have to run to the bank just to get a copy of last Thursday's version of an project file).
