Haemphyst hit it on the head. Ditch the Panasonic Head-unit. I sell Panasonic and Eclipse and let me tell you that the sound quality between the two are night and day. Don't get me wrong I love Panasonic and have always loved Panasonic, but since I have the opportunity to compare these units with others on the market, to me, they sound terrible. Please don't tell my customers I said that. lol.
For the Polk db's I'm not that fond of thier sound either. They are unforgiving as to tweeter placement relative to the woofer cone. Too far away or positioned incorrectly and you lose the cohesiveness between the two and you get that "hey there's a tweeter and a seperate woofer" effect.
The back Alpine Type S's have a very strong midrange which makes them stand out like a sore thumb. My personal feeling is that they do not match the sound of the Polks at all. You can mix and match brands front and rear, but the voiceing of the speakers will either work together or against each other. For me the rule of thumb is stick with the same brand and model level (type S, type R, TR series, XR series, etc. etc. ) for front and rear for most of my listeners. When I set up a nice sounding system for my clients who are a little more picky about thier sound, I will step the rear speakers down a grade, keeping within the brand, and focus thier attention to the front.
Usually you can use the back speakers to bring up the soundstage from the floor or lower doors. However, if you have speakers in the back that work against the fronts, then the only effect you get is "gee, those are rear speakers back there." and your focus is lost.
For staging, it comes down to tweeter placement, and adjusting the amplifier, and in some cases, the crossover network that come with the front components. Some crossovers have some adjustablility to them, allowing to increase or decrease the tweeter level relative to the woofer. Don't be afraid to experiment with your placement. When I'm setting up a system I can spend an hour or two just messing with placement and sound staging. And when it comes to this stage in the install, ditch the test tones! Use your tones to set your gains to a GENERAL level, but then use some actual music to do your final adjustments. Music that you are playing will also be a major factor.
For me, ditch the iPod for testing. Go "old School" and grab a CD. You'd be amazed at how many people don't realize that when they download thier music, the fidelity of the files are crap. Now I'm not saying this is the case, or that you can't get good sound from an iPod, but it's just another variable in the equation that I can completely eliminate. Get a CD that has been "remastered" or has been produced in the last five or so years. Older CD's from the 90's and even 80's have unusually low recording levels to give the music more dynamic range. Also, grab four or five different recording artists with different genre's. But mainly, be true to your listening style. One question I NEVER ask a customer is "what music do you listen to?" why? because they always say the same thing "everything." Well no you don't. You may listen to Tim McGraw as you're scanning through the radio stations, but your CD case is loaded with nothing but R Kelly, TuPac, Yukmouth, and Too Short.
All in all, it comes down to your ears. I can set up a $5000 system for SQ, and half of my customers love it and the other half hate it. We all hear differently. One last thing. No matter how hard you try, how much money you spend, or how good of an installer you are, you will never, never, get a system in a car to sound great with every type of music. You can get close, but face the facts that some of your music will suck compared to others unless you tweak your system every time you switch CD's. It's not a "set and forget" kind of hobby.