Sorry its so late in my response. Had a busy night at work. Still here tho
Ok so I will answer the "what music" question first.
This can be a bit tricky because just like cars, every piece of equipment is different. Something that might work for some might not work for others, what some people think sounds right may not sound right to others etc.
When I am tuning a car audio system, I focus mainly on the kind of sound I want and the music I will be listening to mostly. Now I still use some other tracks of different genres but if your going to be listening to mostly rock, you dont want to use bass heavy rap to tune with.
I usually will do my first tune with a very broad ranged insturmental track of any genre. One track I have found that is a great starting point is called "Requiem For A Tower".(youtube it, you all have heard it, just may not have realized it) It has a very broad range of sound from low bass's, beating drums, violins, horns etc.
Start by turning off or disconecting any subwoofer, then turn the system to the maximum volume that you start to get distortion and then back down 1-2 "notches". Tune your bass frequencys first as they will be what will cause the most distortion. You will likely start to get distortion turning the bass up since you are so close to the threshold so simply tune, turn down, tune turn down etc. Also, if you are running a sub with your system, turn the bass down another notch or 2 from "what sounds right". You want to do this because again, the lower bass frequencys are what cause the most distortion and you will have a sub to "pick up the slack".
Next tune your midrange frequencys if you have this option on your deck. (most new ones do). Again follow the same logic, tune till you get distortion, volume down, etc. If you do not get distortion then you do not need to turn the volume down.
NOTE: You want to tune to where sounds blend and are crisp without overloading or overpowering other sounds. This can be a bit tricky for the untrained ear. Just as a general reference point, I find that with most decks if you are running a sub as a good starting point, set the bass to minus 2-3, the mids to around positive 2-3 and the treble to positive 2-3. Frequency range that is good for 6.5" fronts and 5.25" rears that we have in the 4 runner are between 90-120 hz bass, 500-800hz mid range and 7khz to 12khz for your treble frequencys. Again, its going to come down to blending your sounds for the type of music you listen to.
The next step is to change tracks to a more bass heavy track that utilizes the type of bass you will be listening to. If that is punchy rock type bass, find a good insturmental track that has a good double bass drum "riff" in it. Turn your sub back on and play this track a few times while adjusting gain and eq settings on your amp. Turn the gain/bassboost all the way down on your amp, turn your system till you get distortion, then back down a notch or 2. Now adjust your gain on your sub until it is creating a decent amount of bass but not that it is close to distorting. Around 50-75% of what your sub can handle. Tune your frequency to the desired sound. (Rock tracks around 55-65hz, boomy rap 35-50hz etc. This will also vary greatly on they type of box you have "ported or sealed" the box tune, the size of your woofer, vehicle size etc so again you will have to listen closely to what sounds right for your tastes.)
Once you have found the proper frequency for you, adjust the gain up until you start to hear a slight distortion. This can be very hard with a sub because distortion can be confused with air movement. There isnt a great way to distinguish distortion from air movement and box resonation however, if you listen closely, you will hear almost a "buzzing" from the center of the sub if it is distorting.
When you reach your distortion point, turn it back down slightly. One thing to remember is that subs need to be "broken in". The proper way to do this is on a test bench in an open air enviroment doing frequency cycles however most people dont have the time or equipment to do this. To break in a sub in car, in box, the most efficent way is to play a very bass rich track that ranges in low end frequencys. Play this for around 1-2 hours straigh if possible at around 75% volume. Alot of older blues/bluegrass/funk tracks work well for this because they focus alot on the bass guitar and use many notes on it. (think of the bass rift's in "Play That Funky Music White Boy" or "Low Rider".(the focus of breaking in a sub is to get the voice coils hot enough to "burn off" any contaminates, foregin matter etc, as well as to "loosen up the surround and cone so that they are flexible) again, a subs entire purpose is to move air so the further the cone can travel and the more it can "conform" to different frequenctys, the louder and cleaner it will be.
Lastly, place in the music you will be listening to most commenly. Turn it up to around 75-90% volume and make slight tweaks to accomidate vocals. You should at this point however be very close to where you need to be so if it sounds way off, you missed something somewhere.
Well that actually looks like I covered both questions at once lol.
2 things to remember, if you are using an external amp for your fronts and rears, turn the gain all the way down, the deck to around 75% of maximum, then the gain up on the amp.
Also on your sub amp, if you are having to turn your gain more than around 70-80%, you need to look into a larger amp. Turning the gain to the max to get the sub to peak will cause the amp to work harder than it should and create excess heat and electrical interference/distortion.
If there are any other questions, I will gladly do my best to answer them.
And yes, those polks will do fine also. Didnt see those originaly otherwise I would have stated the should be ok. The only problem with polk is they have 2 "lines" of their products. There average consumer line for you everyday consumer who wants the polk name (they are still good speakers though) and then their audiophile line. They dont tell you there is a difference but walk into any true home theater store and you will see and hear the difference between the ones they have there vs the ones at best buy for half the cost.