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.
When it comes to conspiracy theories, I tend to take the advice God gave his prophet, Isaiah: "I'm warning you! Don't act like these people. Don't call something a rebellious plot, just because they do, and don't be afraid of something, just because they are. I am the one you should fear and respect. I am the holy God, the LORD All-Powerful!" (Isaiah 8:11-13, CEV)
But I gotta tell you; some of the "off the radar" developments swirling around on the periphery of the Michigan Dele-Gate fiasco have me wondering just what the hell is going on behind the curtains in those back rooms. And specifically one development has me intrigued.