The Start and End buttons are used to simplify the comparison between the initial and final structures - Start resets the current animation to the first frame, and End jumps to the last frame. If you need to jump to a specific frame, enter the frame number in the Jump To text area and press enter. One thing to bear in mind is that the frame number starts at 0, so to jump to the 5th frame, you must actually enter 4 here.
All of the controls affect the active molecules, but two parts of the animate menu use information from the top molecule. There is a display just below the End button which shows something like 0/1 or 23/59. The first number specifies the current frame number, starting at 0, and the second gives the total number of frames.