The two wires from the speaker you intend to mount on the right side of the parcel shelf will connect to the two wires labelled "Right Rear", or similar, on the back of the head unit. Likewise, the two wires from the left side speaker will connect to the two wires labelled "Left Rear", or similar. If you don't know which wires are which on your head unit you have a problem. Generally, you have two rectangular connectors on the head unit. One connector has about five or six power cables (red, black, yellow, orange and the like (blue is for electric aerial)). The other connector has eight cables for the speakers. They will be in coloured pairs, and one of each pair will have a black stripe down it. Each coloured pair goes to a speaker, one in each corner of your car, and the wire with the black stripe is the negative wire. To find out if you have the right speaker connection turn the head unit on a play with the balance and fader controls, you'll soon know if you're connect up wrong if your unit is set to right rear and sound is coming out of front left.
It doesn't matter which of the two terminals (large or small)on the speaker you connect the black striped wire to as long as you connect all the speakers the same.