Atmel have a board available for their STK600 development kit (Atmel.com). With some modification the board can fit to an Arduino on the standard headers, and have bootloaders burned easily.
A good alternative is available on ebay (here). However you will need to add a PCB to adapt to Arduino headers.
Oscillator circuit (crystal, capacitors and resistor) connected to xtal1, xtal2 and GND.
Birdsnest of interconnecting cables from the Arduino headers.
Closeup of MEGA328P in place for programming
Remove the MEGA328P from the Arduino
Mount the AVR board to the Arduino
Hook up the set via USB to your PC then use the following to program the TQFP32 MEGA328P
That gets the bootloader onto the chip.
You will need to include a header on your PCB to access TX, RX, RESET, 5V and GND to program the MEGA328P from the Arduino environment, using an Uno to pass-through the signals, or a standard ICSP header for programming via Atmel Studio and an AVRISPII.
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