Whatever works best for you! Just a short comment: you can easily combine the 4 for loops in your code example into a single one without pushing the commands into an array of commands, just increment $i inside the loop then do your tests for i%2 using one if-else control structure.
The whole set-up still looks awkward to me but that doesn't matter and you should go with it if it works. After some more experience you might come back to this and then immediately see a better way of doing it. If I now look at some of my early Perl scripts it causes me physical pain :-). It's just the way it is. Good luck with your further adventures in Perl!
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