The reasonable doubt applies to whether or not he shot Martin. There is no reasonable doubt that he did. Therefore in order for an acquittal, he has to convince the jury he acted in self-defense. Or, the prosecution must create enough doubt in the jury's mind that his version of the events are true. The crux will likely come down to who was acting in self-defense, and that all comes down to his credibility.
As Schlzm pointed out, it is just as easy to believe that Zimmerman initiated the confrontation by physically shoving or grabbing Martin, in which case Martin would have been acting in self-defense.
Zimmerman lays it on thick about the things that Martin was saying to him, specifically "I'm going to ####### kill you" and "You're going to die tonight mother####er." but none of these things are audible on the 911 call where we can clearly hear someone yelling for help, and this according to Zimmerman occurred when Martin had his hands over Zimm's mouth.
Also, the things he has Martin saying here set off my BS meter in a big way. They're too perfect. It's like lines from a (bad) movie. Especially the "you got me" straight from a spaghetti western, but that is just my opinion.
Now, if I can spend about 1 hour online and come up with this many instances of Zimmerman saying things that either contradict himself or simply don't make sense, imagine what a semi-competent prosecutor can do over the course of a year.