As far as quality and value, I'm a big fan of Yamaha. But also, one of the best sounding acoustics I've ever picked up was a Godin. They may or may not be in your range (and they may not even have and on-board pickup), but they also make a "value" brand, Seagull. Those sound nice too.

Regarding the difference of amps, in general acoustic amps are supposedly geared to better reproduce the higher frequencies and harmonics of an acoustic guitar, while electric amps are more lo-fi, and usually intended to distort, which is great for electric guitars, but not acoustics. The difference would be their wiring and speaker cones. This is a broad generalization though...some amps prolly work just fine, others won't. Keyboard amps are also commonly used. I'd guess LATS would know the most about this sorta thing.