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.
As a matter of lifelong religious preference I'm a Confessional Lutheran (specifically, WELS), a point I may have made once or twice before on this site. I recall well the catechismal training where such questions as, "What does this mean?," or "How is this done?," or "Where is this written?" were routinely asked in such a way as to prod the minds of middle-school-aged youth to master the basics of sound biblical doctrine.
Given what I am currently seeing as a predominant tendency to completely misuse a key in-party philosophy (as well as an apparent misunderstanding as to how that philosophy is to be applied), I find myself compelled to address it similarly.
