The shop should have set you up correctly on the bike when you bought it. Seat position is adjusted according to a combination of leg length and knee position relative to the bottom bracket. Once it's set correctly your reach needs to be set up by adjusting the stem length.
I do this in 3 stages; it's easiest with the bike set up on a trainer:
1. Seat height (center of bottom bracket to top of saddle measured along the seat tube) should be somewhere close to 0.883 of your inseam measurement measured barefoot floor to crotch with your feet about 6" apart. Add 5 mm if you use clipless pedals. You can set it a little bit higher if you wish, but make sure you're not rocking or bouncing at higher pedal cadences. You should have a 25 to 35 degree bend in your knee with the pedal at the 6 o'clock position.
2. Seat fore/aft position should be (at least at first) set up so that, with your pedal at the 3 o'clock position viewed from the side, the little bony lump just under your kneecap is directly over the pedal spindle. Use a plumbline to adjust this. Set the seat parallel to the ground using a carpenter's level to start with and adjust this as needed to achieve maximum comfort.
3. Now you're ready to set up the reach. You really do need a trainer for this part! Sit on the bike, feet clipped into the pedals and spin lightly for a minute or two with your hands on the brake hoods, elbows slightly bent. You should feel comfortable, balanced and have no sensation of stretching or straining to reach the hoods. If you feel you're stretching, the stem is probably too long and needs to be replaced with a shorter one. If the stem is way behind the hub it may be too short. The "can't see the hub" test is a really rough rule of thumb and doesn't apply to every rider.
The best bet? Go back to the shop where you bought the bike and have them check your position, or find a local licensed bike coach who will help you get set up, usually for a modest charge.
Positioning on the bike is really important to avoid injury and discomfort so it's important to get it right!