To the OP's question - I don't know if there's an outboard amp, or if it's integrated into the head unit (hope not). In the Accord, there was an outboard amp, and IIRC, it's located in the passenger-side kick panel up front (the lower area just in front of the door).
I have the service manual for the '06 Civic Hybrid on order; once it comes in, I'll know for sure how the amplification is set up (that's how I knew about the Accord -from the service manual).
On speakers - I put a set of Boston Pro60's (6.5" components) in the front of the Accord, and it sounded like a different car

In that car, I had them steathily mounted as coaxials - I'm seriously thinking of mounting the tweeter outboard, this time around - maybe in the top of the door panel (the A-pillar contains side curtain airbags, and I don't want to mess with those too much - not to mention potential safety issue if they (heaven forbid!) ever have to be deployed). Those were retreived from the Accord, and they'll soon be installed in the Civic.
I also had a set of Boston SL95's (6x9 triax) in the rear of the Accord, but can't use those in the Civic (looking to get rid of them now). You just need something for fill in the rear - so you don't need to spend a ton of $ on the rear - something that gives good mid-bass output. I've not heard the OEM 'bass system', but outside of a few very high-end manufactuer systems, I think you can generally do better, soundwise, in the aftermarket. For your fronts, get the best sounding speakers you can afford, IMO.
Amplification - In the Accord, I did nothing more than have the speakers wired up to the factory head unit. It was good - but if I'd kept the car, I would have proceeded with an outboard amp. I will definitely do this with the Civic - what I'm unsure on is if I want to do a 6-channel, and have it in 4.1 mode, or separate amps for full-range /sub, so that I can disconnect the sub if I need more room in the car to transport people / things, etc (haven't decided if I want an in-cabin sub, or a trunk-mount). For subs, I hear the Infinity BassLink is supposed to be pretty good (from an SQ perspective), but I'd need to hear one (and CircuitCity is not the environment for that

I'm looking for SQ, rather than SPL; your needs may be different
The other thing I'm looking at is a JL Audio CleanSweep, to take the pre-processed DSP signal coming out of the head unit / amp (the Accord has its DSP chip in the amp), and feed the outboard amp(s) a clean, unprocessed signal again (although, when you think of it, if you process a processed signal, that's not 'unprocessed' - that's 'further processing'). But I've heard nothing but shining reports of this device, and will likely try one out.
One other thing - the person who mentioned the 'higher-powered' system in the Civic Coupe (EX, Si) - that is the same amplification on the full-range - the extra power is a second 190w amp, dedicated to the sub mounted in the rear deck. I listened to one of these twice - once in an EX, the other in an Si - and I wasn't impressed, either time.