I wonder if a basic point here still needs clarification:

I am creating a basic Perl script ... to automate a few different Unix commands that need to be executed in a specific order.

Using system() to call these commands:

system("nohup scripts_pl/RunAll.pl &");

Do the commands invoked by system need to be executed in a specific order with respect to each other or does the calling script want to run them in parallel before it moves on to other processing? If the invoked scripts need to run in order or don't need to run in parallel then codiac's post may be all you need. If it is the latter case then we need to look at somewhat a more involved approach like some of the other posts suggesting open, shell process control, or fork.