OK, from what you've posted 'till now, the basic structure would be something like this (pseudo-code)

Read numbers from file
Process them
Create output files
Create array of commands to run
Total processes=0
While there are commands left
    pop a command from the stack
    fork() a subprocess
    In the child
        system() the command
    In the parent
        Total processes++
    If total processes >= 4
        wait() until any process returns