Yamaha Sound Reinforcement Handbook...great book to start with. It goes through the physics of sound reinforcement. Not much enclosure acoustics, but everything else is there. It applies to car audio just as much.
Testing phase by ear is rather difficult. Just like engine building, you have to look at a stereo as an entire system. So, when it comes to phase of a subwoofer, conflicts between that and your other speakers are little if the overlap in frequency production is little to none. However, that's not always the case.
Here's the problem w/sub phase controllers...they offer 0 and 180 degrees. That doesn't do much at all. To really control the phase, you need to adjust it between those. Time and phase...by delaying time, you change the phase. Alpine decks have this capablility (some that is) as well as others. The best way to set that is to measure the distance bwt. the sub and listener, and do the math from there. People will tell you that reverse phase is best for the sub if it's facing x position or whatever, but that really is about the same as someone saying AEM makes the best parts, period. See where I'm going...
Again, this same theory applies to every speaker in your system. I should mention that there's another way to test for phase, but requires the use of much more expensive equipment. Keyword though...look for a device that can test "time delay spectrometry" in its features (TEF is the main one). However, I wouldn't expect anyone to shell out the $ for that. Instead, if you have a pocket pc, many companies are making really powerful pieces to add-on to this that can do many of these features (not sure about TDS yet though).
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Freq. response of a speaker...sub in an enclosure...best way to test response is again, w/a proper testing device. Always use the right tool for the job...i.e. don't bring a knife to gun fight. If not, by ear works if you have trained your ear, which takes some experience (re: lots).
Crossover points...this is all based on each setup again. And another can of worms that I don't want go into yet, heh.
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Parametric EQs...instead of typing, I need to find a good link for this stuff.
Any thoughts on what I've typed out yet? Anyone? Is this worth it, haha...