whoever the "guy in the shop" is, i suggest you don't buy from him again. don't look at peak power ratings on equipment over rated power handling, peak power can often not be achieved, and you'd need a lack of real world physics for peak power to play an important role. the amplifier will run the sub, but not as well as it could be running. as a heads up, don't choose fusion or sony, go pioneer or kenwood or JVC if shopping around for basic audio equipment.
in terms of power you've got to play with, run your sub on a bridged channel to get as much power as you can. my ghetto setup which i'm using now until my new equipment i'm using arrives is running a pair of US audio subs, which could easily handle 300 watts RMS each, running on a single bridged channel putting out around 200wrms (watts RMS), and they dont sound too bad.
in terms of those 6x9's, run them in parallel to your second bridged channel, to achieve a 2 ohm load. your amp will probably say to only use an impedance load of 4 ohms on a bridged channel, but 2 should be fine, it is on my cheapy amp anyway, it'll just get a bit warmer than usual. running a pair of 6x9's off a head unit isn't utilising their full potential. a 6x9 will typically rms at about 100 watts, if it's decent, so you shouldn't be stretching them too much. just check to make sure that the ~200 watts the amp will be supplying to them wont be too much for them to handle. for your front speakers, they'll be ok running from your head unit, as a standard stock car speaker runs constant 20 watts of power, and a head unit's amplifier will put out around 18 watts rms of constant power. they will probably not keep up with your 6x9's and sub, so an upgrade might be in order if you're after more sound.
that's a very basic overview, i didn't cover many aspects. for a daily driver that produces some decent sound, it should be doing ok. for info on how to connect amplifiers etc., have a look on the net, there's some good diagrams around, i suggest www.termpro.com, www.the12volt.com and www.bcae1.com, to name a few.
best of luck
experience, and a lot of research over 3 years