From
NCAA ready to make pitch clock mandatory - College Baseball - Rivals.com:
A pitcher is given a warning the first time he fails to throw a pitch by the end of the 20-second clock, and a second infraction results in an automatic ball. A hitter stepping out of the box inside five seconds of the clock striking zero would first be given a warning, and a second infraction would result in an automatic strike. For the between-inning clock, a team failing to be ready by the time the clock strikes zero would be penalized with either a ball or strike.
After going to three games so far this season, I have to say I really like the pace increase from this rule. I have yet to see any drawbacks.