Annotating over PowerPoint is quite a straight forward process. If you are using the Oktopus software, open Oktopus, open SpowerPoint, run the slide show and you will find the Oktopus tools are floating over your slide show. The same process can be implemented if you are using TouchIT Notes.
The third way you can annotate over PowerPoint is if you use the built-in tools that PowerPoint provides. You can find the pen at the bottom left of the screen. In this way, you can use the pen and embed your annotations directly into the PowerPoint file.