An improved system and method for pen-based handwritten and keystroke data input into a computer system is disclosed. The system and method receives pen-based data entry from multiple related input boxes within a handwriting area on a digitizer pad. Thread-based processing allows each input box or group of input boxes to be separately evaluated, providing for continuous character recognition. Character strokes entered into each input box or group of input boxes are saved and interpreted together to allow more complete recognition of naturally written characters. Improvements on keyboard layouts are also disclosed.