Sound is a wave, right? So, it has peaks and valleys. If you play a single pure frequency, the sound wave looks like a sine wave (just like an AC signal, because it *is* an AC signal). When you send the audio signal through a crossover, the components in the crossover (capacitors, inductors, etc) affect the phase. Each "order" of a crossover shifts the phase 90 degrees. So, a "2nd order" crossover will shift the phase of the sound by 180 degrees. That's the same effect as reversing the polarity of the speaker wire on the driver.
The crossover is not a hard cut-off between the woofer and tweeter. There is a slope to the reduction in signal around the cutover frequency. Anywhere that two speakers are operating at the same frequency, if they are 180 degrees out of phase from each other, they will be cancelling each other out. You can be creating holes in your frequency response that will sound weird. By ensuring the drivers are still in phase with the crossover in place, you avoid that weirdness and everything sounds right (or as right as it can!).
Just to add a bit more, speaker design can be a VERY complex subject. Even something as simple as a crossover will make your eyes glaze over.
Quite frankly, this is why most people just stick to very well known recipes for speaker designs. There are "cookbooks" of speaker recipes that you can find online or at Parts Express, Amazon, etc.
I'll probably get started with this book:
That enjoythemusic link mentions a program called sound easy and its apparently not noob friendly.
A few people over at diyaudio reccomend lspcad for noobs and soundeasy for engineers.
Looks like I'll just have to use sleep mode on my computer (You can't save projects on the demo version.)
Thanks for the help.