Uploading with Atmel Studio 6

grumson:
C:\Program Files (x86)\Atmel\Atmel Studio 6.2>C:\Program Files (x86)\Arduino\hardware\tools\bossac.exe --port=COM37 -U false -e -w -v -b "C:\EMBEDDED PROGRAMMING\AtmegaAVR\AtmelStudio\DUO\ARDUINO_DUO_Led_13\Release\ARDUINO_DUO_Led_13.bin" -R
'C:\Program' is not recognized as an internal or external command,
operable program or batch file.

You need to escape the spaces in the directory names and file names. Try adding quotes around the names with spaces.

C:\Program Files (x86)\Atmel\Atmel Studio 6.2>C:\"Program Files (x86)"\Arduino\hardware\tools\bossac.exe --port=COM37 -U false -e -w -v -b "C:\EMBEDDED PROGRAMMING\AtmegaAVR\AtmelStudio\DUO\ARDUINO_DUO_Led_13\Release\ARDUINO_DUO_Led_13.bin" -R