I think what you are looking at is on the quark-d2000-customer-reference-board.pdf. It's on section 2.4 as shown by Table 2. SoC Pin Mapping.
Is that the table you looking at ?
PIN_OUT =0 is labelled as 10 on the silkscreen of the board. In writing the code, you will be using User Mode 0 and in reference to the board is the Arduino UNO R3.
In the May 2016 version of that document it's in section 2.5 Table 2. It does have the Arduino pin labels with the GPIO user mode 1 values.