The compiler for AVR processors outputs a HEX file, which you can save to wherever you like. Loading a HEX file into the on-board FLASH requires a single command line, running avrdude, which you can see by turning on verbose compile. Put that command line, with a few edits, in a Batch file, and you can upload the HEX file to the board by simply running the batch file.
Regards,
Ray L.