I'm agree with you, documentation. The most useful thing at the present is looking at examples of software implementations and reading datasheet.
I understand that you are looking for a document that explains each command for the development kit, unfortunately, the Intel Quark Microcontroller D2000 datasheet is the only document available.
As Lockdog pointed out, reading the datasheet and analyzing the examples is the best way to learn about the specific commands.
Please refer to the QMSI API documentation. In the latest ISSM version it is installed here:
C:\IntelSWTools\ISSM_2016.1.067\firmware\bsp\1.1\doc\pdf\Quark Microcontroller Software Interface 1.1.pdf
Looking at the actual QMSI implementation (*.c and *.h files) might also help.
That's what I was looking for, thanks!
Thanks everyone for your replies!