Ok, well I have read the manual, and as ridiculous as this sounds, the guy from JL is wrong. Now for the last time, I will tell you, your input needs to be on HIGH, and I am going to take one more attempt to explain to you why.
LOW INPUT: is for 200mv-2v inputs.
HIGH INPUT: is for 800mv-8v inputs.
Now your HU is feeding 5v signals, which even if it is not a true rating, it may be, what? 3.5-4v? So even assume your HU is only putting out 4v. You tell me, using simple logic, where your signal falls into? The low input, or the high input?
You have 4 volts, do you fit between 200mv-2v, or 800mv-8v?
You need to be on the high input. Otherwise, you will be feeding your subwoofer an exceptionally strong, and clipped (very bad) signal. If you want to run it on low input your subwoofer will fry. If you don't care about the lifespan of your subwoofer, then run it at low input. Just know, low input is the wrong setting for your amplifier for your subwoofer.