Well if it's running then you've already got the CDI wired correctly which means all you have to do at this point is take one of the wires from your kill switch (doesn't matter which one) and join it into one of the CDI wire connections, so you have 3 wires coming together. The other kill switch wire needs to be grounded to the bike, I just loosend a muffler mount nut, wrapped it around the bolt and tightened it back up.
On my bike it is...
CDI black wire to ENGINE black wire
CDI blue wire to ENGINE blue wire and KILL SWITCH blue wire (three way connection)
KILL SWITCH yellow wire to muffler bolt
Make sure you keep the tip of the white wire taped up until you decide to use it or it could come in contact with the frame and kill the engine.