First of all, just because a car has a place for a speaker from the factory doesn't mean it HAS to be filled. Second, if you install a subwoofer into the trunk of your car and the trunk is sealed from the cabin of the car (i.e. no place for the pressurized air to go) the forces the sub creates will be wrought on whatever surface it comes in contact with. With 6x9 speakers mounted in the rear deck of a car it's the cones and because the sub is larger, moves more air and has a good deal more force in doing so than the speakers it will move the cones of the 6x9's. That leads to damaged and destroyed 6x9 speakers. Installation is the key in that case. If you can build the sub and it's enclosure to seal up to the cabin of the car at the back seat so that it never pressurizes the trunk then the previous point is moot. No matter what the 6x9's should still only be used for rear fill, or in other words only to play the ambient background reflections that are picked up by the microphone when the music is recorded. There's no good reason to spend money on an amplifier for them to perform that role. Use that money in other places it will be needed such as to buy better front speakers, sound deadening, etc. Capacitors don't work because they don't CREATE power, they leach it. A capacitor has to be charged by the vehicles charging system and it then stores that power inside it. When the voltage drops a little the capacitor will discharge slightly which in turn "stiffens" the voltage or doesn't let it drop but the help stops right there. That little added help lasts for an instant, a split second, that's all. It's voltage will drop with the rest of the system and then when the current demand is over the charging system has to charge the capacitor along with the batteries and everything else. Do that over, and over, and over again and all of a sudden it's no longer doing ANYTHING to help and is hurting because of the load it's creating on the charging system. IF you truly need to upgrade something in your electrical system it's NOT with a capacitor. Start with a GOOD strong starting battery, BIG 3, and clean every ground connection between the engine, frame and body that you can reach. Then if you're still having voltage problems typically it's cheaper to add a second battery than it is to upgrade to a HO alternator. The second battery will help provide additional current during the big demands, but considerably more so than the capacitor but it too is still a load on the system. If you're at the point that your current alternator is unable to keep up with the large demands, especially for prolonged periods then you'll have to look into upgrading it. This is a rough and crude explanation of how all this works but I think it's easy enough to understand. You've not mentioned what kind of power you're looking at running total. Most people are okay with up to 1,500 watts of power on the stock electrical with no extra batteries and sometimes no extra upgrades at all. It's completely dependent on the vehicle, the amps being used and the listening habits of the person. Every combination is different and has different results so it's best to throw a voltage meter on it from the start. Then monitor it and upgrade your electrical as necessary. Going active is when each and every speaker set, usually separates like components, are connected to their own amplifier and each has it's own crossover controlling the frequencies they play. An example would be a pair of tweeters on one amp, the mids on another amp and the sub on another. It takes a processor of some sort to control the crossovers for each set of speakers and a great deal of time listening, adjusting, and tweaking these setups. They're not for beginners and not what you were thinking before this. The idea is to give the user control over every aspect of each set of speakers that cover a specific range of frequencies so that they can be utilized correctly and blend together for a more harmonious response. Your speaker and sub wiring size is fine, unless you're looking to run 3kw or better to your subs, lol. Unless you're looking at running really high power there's no need to worry that much about the wiring size to the subs or speakers. In most daily listening applications those two sizes are fine for those applications. Try to find a substantial piece of steel to connect your ground to. The heavier the steel the better it can flow current. Locations like the tops of the rear shock towers are heavier steel and make a better location to ground to. When it comes to amplifiers in a car it's all about current flow. The better the current flow the better the voltage stays up and the cooler everything operates. Bad grounds and other connections have resistance, resistance leads to voltage drops which in turn increases the current flow and creates heat. Ever seen pictures where people have had a fuse holder melt? That's due to a bad connection and the resistance it causes.