Digital pins on Arduino function as both positive and negative terminals?
The answer to your question is basically yes, you can use ATmega I/O pins as +/- power supply terminals for other circuits. But there's a limit to what you can power that way (20mA per pin and 100mA total per ATmega). In practice this means you can only power the simplest circuits (single LEDs per pin, and not many LEDs in total, for example). As a general rule, you should really look for other ways to power anything else.

Also, there's a problem with the citation you gave. That 40mA figure is the absolute maximum current per pin, but that should be avoided. Safest is to use about 20mA of maximum current per pin. Also, the ATmega pins should not have more than 200mA flowing through Vcc and GND (also an absolute maximum that should also be avoided).

Usually, you should either power other stuff off of the regulated +5V that also feeds the ATmega (up to the regulator capacity that depends on the Arduino board - 500mA for the Arduino Uno - 1A for LM7805 regulators - and so on). You could also use the unregulated power in some cases. Then you should use digital pins on the ATmega to switch transistors on and off which in turn will switch your load. Sometimes you can use transistors to switch relays, that in turn will switch even larger loads.