how to edit an array in cfg file without changing structure and execute pipe command

i have a cfg file that is an array with tons of configurations, i want to create modules where users can manage it per parts using adminlte, so they will be able to fill a form in order to edit some values from the array, i need a clear example to understand it and how to do it. also i want a clear example about how to execute a pipe command from a software in my windows server.