I will be purchasing an Atmega 328 SMD to run a 3.3V version of Arduino Pro Mini. However, I am designing my own schematic which integrate other components and sensors…
I want to know if using these modules I will be able to burn the bootloader for the Atmega328 for the SMD version:
I am also interested in this answer. My experience is the pocket AVR programmer comes with a cable already. Also you might have to play around wiht it to make it work.
The DIP packages can be socketed. They can be removed for programming or when you fry it. Putting a 6-pin header on your board for plugging in an FTDI cable to do bit-banging ISP is probably the simplest solution for burning bootloaders. Frankly, if you have a good ISP setup you might find that you can skip the bootloader all together and just burn your hex directly. The cable (e.g. http://www.sparkfun.com/products/9717 ) is all you need for programming and the port can be made from cheap breakaway header (e.g. http://www.sparkfun.com/products/116 ). While I linked in Sparkfun product pages, I do not endorse them as a vendor nor do I recommend against them. Just linking to them for simplicity. You might find better prices on the header from a place like Digikey, if you can navigate their online catalog to a similar product.
My $0.02, unless you are setup for SMD soldering, skip the headache and roll with DIPs. Particularly for prototyping.