System Settings allows you to manage various settings, use System Transfer, and use Data Management.
Data Management
3DS
Here you can manage 3DS extra data, and 3DSWare/"Software".
When managing 3DS Software installed to the SD Card, the title.db is read by the core receiving AM commands. From the title.db file, AM gets a list of installed titles, title sizes and the name of the ".cmd" file for each title, which is used to check the authenticity of the title data(product code, title version, and if an electronic manaual is used, is also kept for each title, in the title.db, but won't be used by the Data Management Utility). For each title listed, it checks if the title is authentic(via the .cmd file). If the title passes authentication, Data Management decrypts/reads the ICN data from the executable NCCH(CXI) and displays it along with the archived title size. If a title doesn't pass authentication, a placeholder icon(light grey with a '?' in the centre), name ('????????') and a size of zero are used. Deleting titles removes the title data from the title.db and import.db, and deletes the directory of the content.
DSiWare
When first using this 3DS creates some management data on SD card. 3DS uses a separate directory than DSi: /Nintendo 3DS/<SomeID>/<SomeID>/Nintendo DSiWare. Filenames are same format as DSi: <titleidlow>.bin. The keys/format for these files are completely different from DSi. A DSiWare export(to SD card) from 3DS is ~0x3bc bytes smaller than an export from DSi.
System Updater
The system updater title is identical to the regular system settings, except only system update is accessible with this. On dev units, this title can only be launched under certain conditions.