According to Scott L. Hysell's PA System Tutorial, the basic setup of a PA system is from a microphone to an amplifier and directly to a speaker. This is actually a simple process if you keep in the mind the direction in which the signal travels. With this basic setup, the signal travels from the speaker or singer into the microphone, from the microphone to the amplifier, and finishing at the speaker, which ultimately projects the speech or music.
In turn, you should plug in the components in an order that reflects this direction. Plug a microphone wire into the microphone, which should be understood as an "output" for the microphone. Plug the other end of the microphone wire into the input of the amplifier. Your amplifier will have inputs and outputs for the speaker wire. Plug the speaker wire into the output of the amplifier because the sound is coming out of the amplifier to the speaker. Plug the other end of the speaker wire directly in to the input of the speaker itself.
More likely than not, you will have an added mixer and equalizer that will sit in between the microphone and the amplifier. The same theory of following the signal direction applies here. When you have multiple components, you want to make sure that the equalizer sits between the mixer and the amplifier. Hysell warms that when plugging in the speaker to the amplifier, you should never plug speaker wire into the speaker's "output" because it will damage your PA system components.
The microphone wire plugs directly in to the microphone and the other end of the wire plugs into any "input" that exists on the mixer. You will also want to plug a "high Z cable" into the mixer's "main out." Hysell indicates that you should take the other end of the high Z cable and plug it into the equalizer's input. Take another high Z cable and plug it into another one of the equalizer's outputs, and plug the other end of the cable into an the amplifier's input. You most likely have at least two speakers, so you will need to plug the two speaker wires into the outputs of the amplifier and plug the opposite ends of the wire into the inputs on the speaker.