1. A method of displaying one or more of a plurality of desktops and applications, each having at least one window, on a multi-display device, the method comprising: displaying a first window associated with a first desktop on a first display of the device; displaying a second window associated with a first application on a second display of the device; receiving, by one or more processors, a first input that represents an instruction to move the first window associated with the first desktop to a non-visible position, move the second window associated with the first application displayed on the second display of the device to the first display of the device, and move a third window associated with one of the first application and a second application from a non-visible position to the second display of the device; receiving a second input that represents an instruction to move the second window associated with the first application to a non-visible position, move the third window associated with one of the first application and the second application displayed on the second display of the device to the first display of the device, and move a fourth window associated with a second desktop from a non-visible position to the second display of the device, wherein the first window associated with the first desktop, the second window associated with the first application, the third window associated with one of the first application and the second application, and the fourth window associated with the second desktop are arranged in a at least one window stack, and wherein an order of windows of the at least one window stack is manipulated by at least a user input gesture that corresponds to a logical order of the at least one window stack in which the first window associated with the first desktop, the second window associated with the first application, the third window associated with one of the first application and the second application, and the fourth window associated with the second desktop are selectively moved to either visible positions in the at least one window stack corresponding to visible positions on the first and second displays or to non-visible positions in the at least one window stack.