If you're talking about the factory speakers, you have a tweeter and full-range speaker in each door, and a sub behind the driver and passenger seat.
It's the speakers behind the drive and passenger seats that aren't working?
Were they working before you replaced the stereo?
If so, it could be that you have a High-Pass filter setting on the stereo that is set to cut low frequencies from playing through the "front" speakers. Since the speakers behind the driver and passenger seats are on "front" speaker circuits, they would be affected by a High Pass filter set to prevent lows from coming through - this would have the effect of making the speakers behind the seats very quiet or silent.
It sounds like you need to check your manual
(located here) or quick reference guide
(located here) and head unit settings to see how you have them set.
See p18 (manual) for setting the Bass Center Frequency and Bass Bandwidth settings.
See p19 (manual) for setting the High-Pass. Try turning it off. Note that unless you wired a subwoofer into the system, the subwoofer settings will have no effect.
See p22 (manual) - Power IC Mode. The factory amplifier in the car expects line level signals (speaker wattage). Your head unit is set to Power IC On from the factory. This is the correct setting. Check to be sure that is how it is set.