Thanks for the reply.
About the first link, when I copy the file to the drive, nothing seems to happen. I've tried .hex files.
About the second link, JLink looks like a good way to go, I'll try that.
EDIT:
The problem that I've mentioned below has been resolved. It was just the wrong pin_mux files in my project. But the first problem remains.
Also I've installed KDS setup wizard addon to Eclipse, I'm able to build the project but when I try to debug, debugger runs but the code is not running on the board. Is there any setting that I need to change in the debug configurations. My current configuration is attached.

