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.