Dive in and allow your brain grow organically. Because anything you put in TheBrain can always be edited and changed, you'll never be permanently locked into any of your early design and organization decisions.
Use "Header" (parent) thoughts whenever you can to cluster related items together. Then jump link the header to related items to help with navigation and finding information later on.
Use a Master Header with a unique icon for major sections of your brain. This special icon will help you quickly locate the major areas of your brain in the instant activation search.
Don't be afraid of nesting your thoughts deeply, with multiple layers of headers, if necessary. This will keep the plex cleaner, and will actually streamline the process of organizing and finding information in the plex.
Use standard naming conventions on your thoughts wherever possible since this will organize the thought display and help you find what you are looking for.
Experiment with using special characters at the start of your thought names. This will allow you to segment similar types of content. For example:
All my main topical headers begin and end with an equal (=) sign: = Current Projects =
Thought names for online stores I frequently visit begin with a "greater than" sign: > Amazon.com
Set Preferences to Show Siblings. Viewing siblings will help you find potentially related items for creating either jump thoughts or new section headers (or both).
Use an "In Box" and/or "Quick Drop" thought headers for adding items quickly when you don't have time to link them elsewhere in the brain. This will create a "holding tank" for thoughts you can later review and organize.
Use a "Temp"(temporary)thought type with an eye-catching color for items you're not sure you will want to keep, or that will need considerably more review and investigation to determine thought type and placement.
Organize dated items by year to reduce clutter and increase the ease of finding what you are looking for.
Archive thoughts that are no longer useful or relevant. I have found this is better than deleting these thoughts since I do occasionally refer to archive thoughts again, and sometimes even reactivate them.
Use tags and link types to further highlight details that will help you locate what you are looking for.