I started using this microcontroller but I am dealing with the lack of documentation. First of all this is the datasheet. It describes registers and their usage but not a workflow. Which one to set first, which second etc. The ASF Get Started quick guides are very limited to high level staff, like USB protocol etc. At last, there are existing examples which demonstrate but it is a mess with out a documentation.
Good datasheets tell you what the part does, not how to use it for whatever your particular purpose is. It turns out your link is not to a datasheet, some product page apparently, so I can't comment on this particular datasheet directly.
If datasheets provided the hand-holding you are asking for, they would get irritating very fast to everyone that didn't care to use the part in whatever particular way the paint-by-numbers instruction say. Not only would that dilute the real information that everyone else is there to get, but any particular recipe will be wrong in a number of circumstances.
The correct procedure is to read the datasheet to understand how the part works. Then you can synthesize your own method of harnessing those capabilities to achieve what you want. Information beyond that really doesn't belong in a datasheet.
This is what app notes are for. They are examples of how to use parts in particular ways. Go look for app notes related to what you are trying to do.