Settings sound good.
Phase can correct acoustic cancellation or "dead spots". this will happen two ways, one is caused by other speakers in the cab, the other is caused by reflected sound from the source speaker.
There are a few ways to set the phase correctly.
The quick and dirty way is to turn the volume up to a normal listening level, then slowly adjust the control back and fourth listing for the point at which it sounds the loudest in the drivers seat. the loudest point will be the most in-phase point, this is the optimum setting. this will get you 80-90 percent perfect.
Another more accurate way is to wire the sub with the polarity reversed, then listen to your music at normal level adjust the **** back in fourth like before. this time you are listening to the point at which you hear the sub the least. once you find the lowest point then wire your sub back to its proper polarity electrically. this method allows for a more accurate setting. because it is easier to hear the differences when your listening for a lack of bass.
You can also do this with a RTA but I wont get into that..
Gain, if you find you need to turn it up real high on the sub, two things could be wrong. One is your head units output level, if you are only using half of the potential volume on it then your not getting its full RCA voltage, you need to be using 3/4 or a bit more of the **** for the strongest cleanest signal. this will allow you to drop the gain back on your amps. and give you best sound.
the other could be that your front speakers are overly sensitive and/or the gain on their amp is set to high. backing down their gain then turning up source volume will feed more power to the sub amp.
Bassboost can be used slightly* (no more then 3-6db if needed) but it will require you to back the gain down a little to prevent clipping. There are cancellations in some vehicles that will cause a severe dip in the 40-70 hz range. so bassboost can be a good thing if you don't have an equalizer. (I should measure this for our trucks)
Id like to mention something else since your using component speakers, since the mids are in the door firing at each other and causing cancellations. I found that flipping the polarity on the drivers side mid (only the woofer, not the x-over or tweet) will increase midbass output, and also center the sound stage for the driver, which really improves the sound up front.
Last thing, since the markings on the controls are not accurate, due to a few reasons. You should not rely on what you think might be correct. You have to let your ears determine the best setting. the markings will only get you in the ball park.
Toreador Red 05' FX4
4.0 4x4 A/Tran Ext.Cab Daily Driver. Nomads, BFG M/T's
Alpine 9857, JBL MS-8 DSP, US Acoustics 2x80w & 2x100w, Vifa 1" XT25 Dual Ring Radiator Tweeters 3k+ 24db slope, Dayton Audio 7" RS180-4 Mid-woofers 100Hz-3k 24db slope, 500w rms Kenwood Class-D Mono - JBL 10" GTO1014 Sealed. 100Hz- 12db slope