The very top level of the database is called the root. The root contains seven tables. Below is an explanation of each one.

root.system
The system table contains all sorts of scripts and information that make Frontier run. Frontier is an application, but much of the functionality exists in the root. This allows for quick updates and rapid changes to the tools that Frontier offers.
For the most part, the system table is off limits. You can look around, but don't change stuff in here! If you customize in here, you risk losing your changes in the next update, because the contents of this table 'belongs' to Userland.
I used Frontier for a year before I even bothered really exploring this table. If you don't want to know what goes on in here, you don't have to!
root.examples
Examples is a table of all the data types that are available in Frontier. This is mostly a place for exploring. This table is often cited in the online verb documentation at scripting.com .
The examples will help you work through the verb documentation. As you become more experienced in Frontier, your trips to this table will be come less frequent. (In my personal root, I've deleted this table--of course, I made a backup, just in case I need it again.)
root.scratchpad
The scratchpad is just that. It's a place for experimenting, and a place for data you don't mind losing. Anything you put in the scratchpad might get wiped out by another script or program.
Because it's a volatile table, no important data should be kept here. Feel free to explore and practice in this area. It's all yours.
root.workspace
Workspace is a bit more permanent area. You can keep scripts and other data here, if you like. Some people create a subtable with their initials in this table, and store all of their utilities in that table, to keep it together.
I use this table for creating scripts. I'll write and test the script here, then move it to a more permanent location once I'm happy that it's working properly. My boss keeps his Director scripts in a table here (of course, they don't run in Frontier, but he likes having a place to organize them).
So, again, this area is for you to manage and control. Think of it as a workshop table, or closet. It's all yours, just don't let the dirty laundry pile up! ;-)
root.user
The user table contains preference information and data used by suites and different parts of Frontier. A variety of settings are available here--probably the most important two are user.prefs, and user.html.prefs. These are environmental preferences for Frontier and for the html framework.
Another interesting place is user.menus, where the custom menu and the bookmarks menu are kept. You can customize these menus to your liking!
root.websites
This table is a special place for all your website data. The contents of this table are discussed in more detail elsewhere. In particular, the web tutorial that was included in your download package for Frontier 5 has a lot of detail on this.
The web tutorial is also available at:
http://www.scripting.com/frontier5/tutorials/web/
Two notes: a lot of important data is kept here. It pays to make backups! Also, inactive sites can be exported (Cmd-3) [Control-3] and then deleted from the root. You can load it in from the exported backup you made. This keeps the websites table light and uncluttered.
root.suites
Suites are groups of scripts that perform a specific function. They are like little mini-applications implemented in Frontier.
Generally, suites are written by more experienced scripters. A number of important functionality is implemented in Frontier suites, or originated as a suite, and then was later moved to the system table. You can access these suites by choosing a suite from the "Main -> Suites" menu.
Next: Jumpin' and Clickin' around the root
Page 1: Frontier's Database Defined
Page 2: The Advantages of Frontier's Database
Page 3: What's in the root?
Page 4: Navigating the Root
Page 5: Where do I keep my stuff?
Page 6: Database Names and Addresses
Page 7: Database Care and Feeding
Page 8: Object Database Tech Notes