You can put anything anywhere, just move as you would with one screen, just think of it as one wide-arsed desktop (or high if choose you to set it up that way). Generally though I set certain programmes on certain screens (expecially at work). What goes on what screen depends on what I need to compare the most.
The best triple monitor setup I've seen was a guy at work who setup his Macbook Pro to work in conjunction with his PC therefore giving him 3 screens, two from the Macbook Pro and one from the PC (all with the same mouse and keyboard) but it all worked seemlessly - very impressive!