1) Your Alpine deck should send a full signal to the Boss self-powered subwoofer. The reason is the Boss self-powered sub already has a built-in filter so there is no need to "double" filter the signal. See picture below. I would turn the LPF almost all the way to the 150Hz and maybe scale back 1/8th of a turn.
You have the bass boost which adds more bass, that is personal, so turn to 6db if you want more bass.
The gain is sort of tricky and needs to be matched with the head unit. If you hear the speaker distorting, you want to reduce the gain. This is a simple way, not very technical. You should turn the volume up to 75% and increase the gain until you hear distorting, and then scale back.
2) As for the infinity 5.25" speakers, those are coaxial speakers and already have a built-in filter so they should receive a flat signal and there is no need to adjust the filters. Adjusting the deck's filters would be more geared towards speakers that are components, when you need to control the audio signal so it works well with the speaker.
3) If you want to change the equalizer, everyone has a different ear for sound. I would play with the Deck's pre-set functions, like Pop or Rock or Jazz, with differen songs that you like to listen to, or radio stations. You will hear the differences between these settings, and each pre-set equalizer serves it's own music purpose. If you want to get technical and really play with the equalizer, you would want a more robust audio system. Keep it simple and do not overthink it. Have you downloaded Alpines' app, Tuneit, for your phone. You can see what others are using for settings and share info through the app.
4) If your Infinity speakers sound "off" it could be due to the deck as the deck's internal amp is rated at 4 ohm and 18 watts. The Kappa52s are rated at 2 ohms and recommended power is 55 watts. These Kappa's could be drawing too much from your deck, and an amplifier may be your next upgrade to make those Kappa's sound better and alleviate overpowering the deck. This would be a great little amp for the Kappas, just google it. - SOUNDIGITAL EVOX 400.4
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