Why do have to turn down Bass eq and how to protect your subs?

[Pyrofan]

Why on most tutorials on tuning a sub do they turn down the bass on the head unit. Can you max it out with a sub installed? Im using a stock HU so it doesnt know a sub is hooked to it. Why cant you do that or is it fine? Also, my subs are under my backseats firing forward. Do i need to cover them? Whats a good thing to protect them at full excursion? I thought of a strainer like for Mac n Cheese. That work?

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