Arduino user code never runs on the x86; that core is only there as a companion to run USB/serial code.
Intel has not published datasheets on the chips/cores themselves yet. However, you can find most of the low level details you need by installing the Arduino101 board package and then exploring the files in Packages/Intel/hardware/arc32.
ARC is the instruction set. ARC (processor) - Wikipedia. However, you probably won't need to know any more than that. All the low level details including direct GPIO register writes are available in the sources you'll find in the arc32 folder.
edit: Also a nice example of low-level ARC code in the NeoPixel library version installed by the Arduino101 package. Look for the "defined(ARDUINO_ARC)" code, it probably does something very similar to what you're interested in doing.