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.
A man who was traveling home following a Campaign For Liberty (Ron Paul) event was detained and harassed by TSA in St. Louis for carrying cash. Yup, for the intolerable offense of carrying currency you too can be held in police custody. Federal tyranny grows on the back of locals who have an ego, and a desire for power over others, completely oblivious to their role to "protect and defend the Constitution of the United States."
They that can give up essential liberty to purchase a little temporary safety, deserve neither liberty nor safety. (Benjamin Franklin, Historical Review of Pennsylvania, 1759)