The result of the coin toss showed which candidate would speak first
Whichever candidate has won a coin toss before the debate will respond
first to the initial question.
From the transcript, we see that Hilliary Clinton won the coin toss to get asked the first question.
Beginning with you, Secretary Clinton, why are you a better choice
than your opponent to create the kinds of jobs that will put more
money into the pockets of American works?
CLINTON: Well, thank you, Lester, and thanks to Hofstra for hosting
Apparently, this is why she was placed stage left (on the right of the audience)
The CNN Republican debate placed Mr. Trump stage center as the leading candidate, and flanked him with the next in order. Similarly, Hilliary got the center position in the democratic debates.
Similarly, she got the right hand podium in the one on one debates with Bernie Sanders.
This might imply that Hilliary got the right hand podium because she is ahead in the polls.
The debates with a sitting president puts the incumbant in that position.
Nixon had that position in the debate with Kennedy (who was regarded as the "challenger")
I have seen references that people tend to pay more attention the their right so that stage left is regarded as more important. However, I do not have a citation for this. However, it would seem that people normally pay more attention to their right.
In slang terms, the right hand is regarded as more important and powerful. Thus being on the right (from the audience point of view) is preferred. You can see this from various biblical references as well. An example is when Jacob blessed his grandchildren. The placement of his right hand showed which blessing was to be "more powerful".