Note that at a certain point, as your skills mature, you may want to integrate the microprocessor used in the Arduino into your design; at that point, it would no longer be an Arduino, though the chip may still be running the boot loader (although in the real final design, you may want to eliminate this, too). If you do run the boot loader, bring out the pins needed for serial communications to a header; that way, in the future (if needed), the device could still be "field-programmed" using an FTDI cable or breakout board.
Realize that the Arduino is just a particular system and layout, based upon a widely used (and low cost) microcontroller family from Atmel; what you do with it is up to your imagination in the end...
