you have to properly set your amp tuning. the gain knob is not volume. read this: How to Adjust Amplifier Gains Using a Digital Multi-Meter | Learning Center | Sonic Electronix
this will tell you how to properly set your gains on your amps. also you need to find the 75% of max volume number on your headunit on the stock (if the non bose uses the same numbers volume with 65 max) the spot you want to set yours is 49 then adjust the amps from that setting. 49 will be your new max. (you do this as most headunits introduce clipping above 75% of rated max power) infinity speakers will have very harsh treble to them its almost unbearable which is why I don't use them, the rest of them is ok but the highs are too high, alpine speakers have a more muted tweeter made of soft materials instead of hard ones like the infinitys and to me alpine speakers produce a better mix of mids and highs together then infinitys do.
Rockford fosgate speakers are similar to infinity that they use hard materials in the tweeters but they have better crossovers in them (coaxial, you have component and have not compared the 2 brands component sets) that keep the harshness down some, though they are still harsh to me. infinitys are the absolute worse for harshness of the reputable brands, turn your treble down. are you using this amp to just power the front 2 speakers and a sub? if so disconnect the back speakers from the system, this will help with sound quality as you most likely cant even hear the rears and wont miss em. (in the stock bose I can tell when the rears are on because the rears do some of the mid and mid bass work for the system, the fronts only do a slight bit of bass and mids most is handled by the rears and sub) you also want to set crossovers in the system use around 140hz high pass or hpf to start on your speakers and 120hz low pass or lpf on the sub after you get the gains set then adjust up and down until you have the door speakers only doing highs and mids and the sub only doing bass (you should hear nothing like guitars or vocals from your sub) and the door speakers should not be doing but some of the higher notes from a bass guitar. so thats a good starting point for adjusting an eq. im willing to bet your issues lie in the tuning of your amp, follow the guide I linked above to properly set them and then adjust the crossover on the amp as stated above.
remember 75% of max volume on the stock headunit is 49 (48.75 actually but round up) so set your head unit to 49 to tune and this will now be your max volume. also while doing the setup make sure your treble and bass adjustments on the headunit are at +-0 and set the gains and crossovers with a flat eq. then you really only want to use the eq to turn down frequencies that are too over bearing, not boost those that are too weak. so if the highs are too much go - on the treble and do the same on the eq on your phone if you use it to set the audio, start flat and then after all the adjustments are in set it how you like but its better to go down on the eq on frequencies too overpowering to match them to the rest then boost ones that are too weak. the crossovers keep the speakers playing what they are designed to play so you use a high pass on the door speakers to cut bass off, 140hz is usually good when you have a sub in the system, depending on your tastes and system you can usually go down to 100hz or so and be ok but keeping it higher gives your sub more range and helps prevent the door speakers and sub from playing the same tone and making it sound off, it also protects your speakers as you start going higher in volume, bass is harder to produce clean then treble (big reason subs take more power) and tweeters typically only use a few watts.
the lower the frequency the more power is needed to match the volume of the rest of the musical range, so keeping that in mind you also want to keep your sub from playing too high range as this can damage it, subs are not built to play above 150-200hz usually. and on a 10" you want it higher frequency to catch more (smaller sub size usually gets more mid bass out of it at the sacrifice of low end bump because it cant move as much air, per example my old alpine type r 12" moved 46L of air in free air while its equivalent 10" counterpart only moved 28L so that extra 2" of cone area moved almost double the air volume) so your small door speakers are not designed to move a 60hz tone like your sub is. and at higher power the lower tones do the most damage when played in speakers not designed for it, again that's why in a stock system people tend to blow door speakers more then the tweeters as the tweeters are not over working the door speaker is to produce any semblance of bass, the bose system has frequency cuts like crossovers for each channel (fronts have it set high, middle one above vents is set very high (treble only, its basically a big tweeter, with some mid playing capacity, the rears play a more full range then the fronts to help the staging and do the mid bass for the system) as the "perfect" car audio system would sound like the band is playing a concert on your dashboard for you.
so think of a concert you face the band and they play in front and the bose system does this well, for some too well, but I like it (its not too powerful hell the whole system has less power then your kenwood amp) but it can beat and turn heads when you tune it right, and I used to have a 2000 watt system in my 08 3 before it got totaled, the bose is 265 watts overall then on your sub you use low pass to cut the mids and highs out again 120hz is a good starting point for a 10" sub, then usually go down to match it and keep it from playing mids but also pick up the mid bass most aftermarket door speakers don't like to do. and again this protects the sub at high volumes. also the human ear can pick up location from high notes better then lows (why the tweeter is up top close to you) and as the frequency lowers the ear has a more difficult time telling where the sound is coming from, this is why the subs are in the back as the human ear cant usually tell the sound is coming from behind with bass it just sounds like its all around. but you know where your tweeters are and how loud they are because they have that high pitch piercing noise.