There is actually an inbuilt serial terminal in the Intel System Studio 2016 for Microcontroller. It has a getting_started.htm guide in the docs folder under your install directory which normally will be C:\IntelSWTools\ISSM_2016.0.027\docs.
In that particular document there is a section explaining how you can get the serial output on terminal.
Regarding your second question, that is a known issue take a look into this site. The use of PWM0 multiplexes the JTAG pins that prevent flashing the board. I suggest you to try the recovery method mentioned in the previous link. Let us know if the recovery helps.