First, you say "I'm running a line out converter from the rear sub to the amp. ", but you can't supply audio signal to the amp, from the speaker its powering (did you mean rear speakers?).
What you need to do is be tapping into the existing speaker system (rear speakers?), or what I do, tap the front speakers right off the back of the deck, and run long RCA's from the deck to the Amp. (I'm proceeding as if this is what you already have done.)
This is how I initially tune sub amps:
Turn headunit/deck volume to lowest setting (not mute).
Remove any "bass boost" or +Bass settings from your headunit/deck (remove any (sub specific) EQ here as well).
Turn off "bass boost" on the Amp.
Set your lowpass on the Amp to around 100-120Hz (you can tweak this later for best sound from your sub).
Turn the "mode" on the Amp to low pass.
Turn the "level" knob on the Amp all the way down (min).
Set the Sensitivity to 100mV - 2V.
Now you should start raising the volume of the headunit/deck to the loudest volume without distorting.
When there, begin SLOWLY adjusting the "level" on the Amp until either your sub starts distorting, or you reach the desired output.
This should provide you with a reasonably "flat" sub spectrum if your speaker and box can reproduce it. If "flat" isn't what you're after, you can adjust the bass levels from the headunit/deck. If you find you need to use the "bass boost" on the Amp, you may need to lower your "level" to compensate, as +15db is a lot of boost.
If your Amp shuts off unexpectedly, it has probably gone thermal, and you may need to reduce the "level" or find a way to keep it cool, sorry offtopic.
Best of luck!
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