The pedals are played with your feet and are on the floor of the console. If you look carefully, they are arranged in the pattern of a regular keyboard, only much larger so that the feet can operate them. The range of the pedal keyboard on most modern instruments is from the contra-C to an F or G two octaves above (although older, Baroque instruments may go up to only a C for exactly two octaves).
The pedals are primarily used to play the lowest line of a score, and usually go down lower in pitch than the manuals by an octave or more. (On many organs, the pedals can also play up as high as the manuals with the aid of couplers and high registers, but such usage is infrequent.)
Most modern organists play the pedals with both the tips (toes) and heels of their feet, sometimes simultaneously if the music requires it.
Because you don't have the same mobility in your feet as in your hands, the pedal part is usually not called upon to play fast, complex music with lots of skips.
You might want to invest in a pair of specifically designed organ shoes to assist with your playing the pedals. Organ shoes are generally black, leather shoes with a narrow heel and pointed toes to make hitting a pedal accurately easier. Most regular street shoes have wide heels, meaning that it's easy to slip and accidentally hit two notes at once with your foot.
If you can't get organ shoes for some reason, you could alternatively try playing in your socks, although this can be hard on the balls of your feet (and there is always the uncomfortable faux pas of having to remove your shoes in front of an audience if performing).