Probably the best reason to use the lpf on the amp would be that it usually allows for finer adjustments to be made.This would be better for blending the sub into the rest of your system.
Try to avoid using the bassboost on both units. but the boost on the headunit may offer more control over what frequencies are being boosted.
I would say, use the gain on the headunit as long as it provides a unclipped signal at all volumes.. its best to send the "hottest" clean signal you can to the amp to avoid interference and noise. You'll still want to use the amp gain a little but not as much as normal.
If your unsure about the gain on the head unit providing a clean signal then just leave it alone and use the amp.
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