Almost every feature of KBiff can be configured from the Setup dialog. What few command line parameters KBiff has are mostly for convenience -- some options just make more sense on the command line.
KBiff revolves around something called a "profile" A profile is simply a container for one or mailboxes that KBiff will monitor. For instance, there will always be one default profile called "Inbox" (or something else if you rename it). This profile will contain one mailbox, usually something like "/var/mail/username". It could just as well hold several mailboxes, though. Each instance of KBiff (that is, each visible icon) corresponds to one profile.