Some of the top menu options only appear if they make sense. For example, if you don't have any visible tools, you won't see the tool control main menu, etc.
For dashboard icons, you need to set them up in Administration -> Detailed administration -> Landing page choices to fit your own facility needs.
If you want to see an example, you can check the demo website setup:
You'll have to remove the /demo/ from the urls however, i.e. use "/calendar/" etc.
Thanks,
Mathieu