A handheld computer which contains an LCD display having a digitizing surface to allow pen input. Internal storage takes several forms, such as a large flash ROM area, battery-backed up RAM and an optional hard disk drive. Several alternative communication paths are available, such as the previously mentioned modem, a parallel printer port, a conventional serial port, a cradle assembly connected to the host computer, and various wireless short distance techniques such as radio frequency or infrared transmission. The computer can readily communicate with other sources, particularly to a host desktop computer, to allow automated synchronization of information between the host and the handheld system. Preferably the remote synchronization is performed at several user selectable levels. When the handheld computer is in a cradle and actively connected to the host computer, automatic capture of updated data in the host computer is performed. Several synchronization techniques are utilized to keep track of different types of files. In addition, while communication is established the handheld computer can enter a remote control mode, allowing the user access to files and applications not included in the handheld computer.