Typically the instrument schedule is organized first by hanging location.
Common hanging locations (or lighting positions) in theater include electrics, apron pipes, front of house positions, booms and ladders.
Within each position, instruments are numbered in the order they are located on the pipe.
While instrument schedules have traditionally been made by hand or on spreadsheets, there are now several industry specific software based means to generate them.
Lightwright is a spreadsheet program that will print nicely formatted instrument schedules.