How to highlight parts of slide and dim the background

There's several different ways of doing this, one of which you'll find in the presentation at the end of this article.

http://www.keynoteuser.com/news/?p=158

I find that when using Keynote it helps to start the approach to an effect by concentrating on the visual appearance of the final effect, rather than starting in concrete term about specific techniques. In that way, it is more likely that I generate a non-obvious but easy way to create the effect, which might otherwise be difficult or impossible to achieve with Keynote's tools.

All of this is a roundabout way to saying that the approach you outline, of covering part of the image, is not the easiest. The easiest approach is likely to cover the entire image you want to darken, and then at the same time build in the original undimmed image on top, masked so that only the relevant part shows. You can do this as many times as you like, and thus have multiple "highlight" sections on the same slide. The Keynote guides make it extremely easy to align the multiple images and then mask the relevant parts, so that they all look like a single image.

This approach is very flexible, and allows all sorts of cool variants. For example, you can take an original colour image, then dissolve in on top of it the same image but with the saturation turned down so that it is black and white, and a third copy in the original colour but with everything masked except an area of interest. The resulting effect is that a colour image will appear to fade to black and white except for one highlighted region that remains in colour. This is a very nice subtle way to do highlighting in images

Alternatively, you can also achieve what you want with your initial approach, if you use multiple slides. On the first slide, construct your masking image with the single hole, and do the appropriate build. On the second slide, construct a new mask with holes for both highlighted sections. Now, to make the second highlight appear, simply transition between the two slides. As long as the slides are otherwise identical, and the transition used is appropriate (such as dissolve, or even none), it will appear as if one slide has now acquired a second highlighted section.