The MultiWii_MotoWii_RevB_V3 sketch needs to be unzipped into a folder called "MultiWii". To open the sketch in arduino, browse into that folder and select the file "MultiWii.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.