There are a number of preferences that can be set to control many overall aspects of the emergent system, including GUI and computation options.
To edit the preferences, go to Root object in emergent and select the File/Options menu on Linux, the emergent/Preferences.. menu on Mac, and the File\Options menu on Windows.
These settings are stored in the user directory under prefs, which is ~/Library/Emergent/prefs on the Mac, ~/lib/Emergent/prefs on Linux, and C:\Documents and Settings\<username>\Emergent\prefs on Windows. The preferences are auto-saved when edited, and auto-loaded when the program starts.
One of the most important settings is the Thread Params for parallel threading (as of version 5.0).
The settings are actually stored directly on the taMisc object, so it has all the relevant information, plus a bunch of other useful routines.