Cleanflight version 1.11 and later include the MOTOLAB target. However, as of the 1.12 release, a pull request to add MPU6000 gyro support for the Cylone has not been added, so Cleanflight from the upstream source can only be used on the Tornado or MotoF3 boards until the maintainer adds that code. In the meantime, I've posted a forked version with Cyclone support added. This version will work on any MOTOLAB target board.
Boards have been shipped with various versions of Cleanflight or Betaflight as development has progressed. I'd recommend installing the latest stable version of either one from the links above when you receive a new board.
The MultiWii_MotoWii_RevB_V3 contains a folder called "MultiWii_MotoWii_RevB_V3". To open the sketch in arduino, browse into that folder and select the file "MultiWii_MotoWii_RevB_V3.ino". Make sure you're in the right place.
config.h should be the only file you need to edit. The only changes you'll need to make might be:
For Spektrum-compatible satellites, the radios may bind at either 1024 or 2048 resolution. The sketch is set for 2048, but if your receiver channels seem scrambled you may need to change #define SPEKTRUM 2048 to #define SPEKTRUM 1024.
To switch from Spektrum satellite to a PPM_SUM receiver, comment the #define SPEKTRUM line and uncomment one of the #define SERIAL_SUM_PPM lines that corresponds with the channel order in your transmitter.
To enable 125uS onshot mode on the KISS ESCs, uncomment #define ONESHOT. You'll need to short the J1 jumpers on the ESCs too for this.