This isn't that hard to figure out.
The countdown timer is preparations for the mission/launch.
The mission starts at T=0
The events leading up to the preparation of the launch/mission are all set according to their distance away from T0… So, T-x. This is why some events are - while some events are +.
After the launch, the mission timer continues. This is where fuel burnoffs, stage separations, rotations, and apogee kicks are timed off of (well, and instruments to verify conditions are as predicted).