I'm not sure in what way you'd like to compare them, but
if you'd just like to view them side by side open both
files and select "Arrange All" from the "Window" pull
down menu. This will automatically create a side by side
layout so you can see all open presentations at once.
You may have to adjust the zoom magnification to be able
to see the entire slide in the window. If that's not
what you meant, you should be more specific about what
aspects of the presentations you're trying to compare.