pre-amp outputs are RCA line connections that are used to connect between a head unit and external amplifiers. you want at least one set of these on any radio you plan to use with an amplifier.
for multiple amplifier setups. front speakers (channels), rear speakers, and subwoofers. having separate channels allows you to have control over balance, fader, and sub output as well as crossover and EQ in better head units like Alpine or Eclipse.