Introduction to Application
Describe what the application/program does and when to use it.
Requirements and Installation
You may want to combine or eliminate some of these sections.
If specialized knowledge is required, like knowing what "samples" are, you should put that here. It's a good idea to refer to the Musicians' Guide, or other existing documents, when possible.
If specialized software, or large software, is installed as dependencies - or especially if it is required but not installed as a dependency - write about it here. Things like fftw or gtk+ dependencies should be left out.
If specialized hardware is required, even for only some tasks, you should write that here.
This is usually "Use PackageKit to install the 'cheese' package".
Basic Use of Application
Ideally, everything would be taught through a tutorial. Sometimes this can't happen, and sometimes it is nice to have a reference.
Advanced Use of Application
More of the same.
Files for the Tutorials
If there are multiple tutorials which use the same files, you should provide links to them here. If there is one tutorial, or if each tutorial uses different files, you should provide links to them within the tutorial sections.
Do One Thing (Tutorial)
Do Another Thing (Tutorial)