Let's take a crown victoria. Rear speakers are under the rear window, facing up. Is that bad? How to correct that?
Unhook them. That'll fix 'em. Then sell them to someone who doesn't know any better.
Rip out everything factory and start over. You want a component audio speaker setup up front, like this one:
http://www.amazon.com/Boston-Acoust...6BLY/ref=sr_1_1?ie=UTF8&qid=1329928858&sr=8-1 Typically, the midrange speaker goes in the door and the tweeter goes in the dash, just because it's easiest. Especially with the little dome tweeters, you can mount them almost anywhere. Run caps in the wiring to filter out the bass, so that your door doesn't rattle. A bass drum thump is ok in a door, but anything lower will make it rattle.
Then your sub goes in the back. Wire it so that it only gets the lower tones, either with caps or through the settings on your amp & head unit. If you have a cheap ghetto sub box that has tweeters embedded in the box, unhook them.
As for brands, I have been out of things for a while. I'm sure there are a lot of decent brands. I like Boston Acoustics for components. The are a lot of good brands for subs, like Infinity, JL Audio, and MB Quart. I used to think Kicker sucked, but they improved their quality a lot in later years. I have two kicker 12's that I'm sure would make me go deaf if I cranked them too much. A rule of thumb for quality of a subwoofer is the size of the magnet. A $20 ghetto 12" sub will have a magnet that is smaller than a hockey puck; my $200 sub has a magnet that's closer in size to a dinner plate.
The size and quality of the sub box will be a factor in the quality of the sound, too. Often they are custom-built to match the shape of the vehicle's trunk or hatch. Your crown Vic uses the trunk as the box for the 6x9s. That's why they sound like they have bass. If you build your own box, use 'medium density fiberboard,' and buy the sub first, so that you can research what the manufacturer suggests for box size. If you don't want to build a box, buy a "free-air" subwoofer and mount it behind the rear seats in the trunk.