A method enables an image to be displayed along with annotations in synchronization with separate, time-based program material as might be found in a computer-based multimedia system. The time-based program material may include audio or video information, or a combination of these, as in a digital movie with the annotated image and movie being accessed from a high-capacity storage means, such as a CD-ROM, and played in separate windows on the same display screen. The method provides smooth, real-time annotation of the on-screen image by synchronizing the movement of a pen image with very low flicker and with little overhead in terms of system performance and memory allocation. This improved performance stems from the inventive use of multiple off-screen buffers, and the processing of the previously stored annotations in the form of multiple data records including temporal and spatial information relating to the annotations as originally performed. The data records are processed during predetermined time periods, with image information being transferred into and out of these various off-screen buffers so as to facilitate real-time annotation in synchronization with the time-based program material.