After some pretty weird errors which would come and go as they please and then a permanent error which would disappear when the user RE-INITIALIZES the tool window in Atmel Studio, I was finally able to select a COM Port from the list (list of COM Ports generated automatically to show only the available Ports) and after selecting an Arduino Board form the Boards list (currently only Uno, Nano and Mega) - I could just click on Build and it would BUILD and UPLOAD to my Arduino board.

Maybe it is not good to have it on Build always, but wont hurt much - I plan to add some more settings and features - tomorrow planning to try my hand at making a VSIX file out of all this so anyone can install the plugin.