You prototype with the arduino and once you have what you want you remove the Atmega chip and use it as a standalone.
For example (for some reason...) You wanted a stand alone system that when you pushed a button a series of LEDS flash.
So you program it into the arduino, get it to work out. Then remove the ATmega chip which ever one you have.
Snap it into a blank PCB wire it up and viola it works; standalone.
Does this work?
If so what pins on the Atmega328 are Analog, Digital, 5v, and GND?