The following 2 commands will help you upload a .bin file from command line using the programming port
mode com7:1200,n,8,1
bossac.exe --port=COM7 -U false -e -w -v -b Blink.cpp.bin -R
you need to add the location of the bossac.exe (somewhere inside the arduino folder) to your path file
if you want this to work from Atmel Studio, You can create a batch file and create an external tools under the tools option in Atmel Studio like this
http://www.jayconsystems.com/tutorial/atmerpt1/
Let me know how it goes..