To help you figure things out, there is a Scoop Admin Guide which can hopefully answer most of your questions.
Some tips:
Most of the layout is changed in "Blocks", found in the admin tools menu
Features can be turned on and off, and configured, in "Site Controls" in the admin tools menu
Stories have an "edit" link right beside the "Full Story" link on an index page, and right beside the "Post a Comment" link on the full story page. They can also be edited by clicking the story title in the "Story List" admin tool
Boxes are what allow you to write new features for Scoop; they require a knowledge of the perl programming language to work with effectively, although you can often make small changes without knowing much perl. If you would like a feature added but cannot program it yourself, ScoopHost does custom Scoop programming as one of its services.
If you aren't sure where to look for a particular feature or piece of display, try the "Search Admin Tools" link in the admin tools menu.
My dear friends, we gather here today to mourn the passing of a good, loyal and stalwart friend of Michiganians. It has looked over us. Watched over us and protected us. But in the end, too many of us were not here when it needed us the most.
It has been often said that "The price of freedom is eternal vigilance."
Sadly, that lack of vigilance is all that was required for those forces allied against us, to take from us, that which we held most dear.