"Ctrl" + "=" makes the highlighted text subscript.
"Ctrl" +"Shift" + "=" makes the highlighted text superscript.
Also, if you go to the Tools Menu/ And click Customize (depending on how it is configed, you might have to click the little arrow point down at the bottom of the list to see everything)/Commands (tab)
Choose format on the left.
Scroll down on the right until you see superscript and subscript.
Click one and drag them onto the tool bar in the main editor to where you want (i.e. next to the bold, italic, underlined mouse click options).
Then with highlighted text, just click those and it will superscript or subscript.
There is also this
http://spectrum.troy.edu/~cking/ChemFormat/If you are "advanced" enough to figure out how to install it.