When using both L/R inputs on a sub you generally get a 6dB gain advantage over using a single input, so that you had to turn down the gain sounds fine. Crossover is actually employed with your sub (rather than just a low pass filter which is fairly common), so if using line inputs with a fixed high pass of 80hz and you dialed the low pass filter to same doesn't sound unusual either. I generally don't use bass/treble controls so making them flat sounds fine, too. Then again a lot is preference....