Administration --> Preferences & Settings are your user based settings (e.g. what you change here will only affect the user you are logged in as).
Under basic settings, you can set things like your printer option, defaults for sending (e.g. whether the signature required tick box is defaulted) and customise your view for integrated orders.
Advanced settings relate to many different areas of the system and are mostly for niche workflows. If you have specific questions about a setting please get in touch with our support team for more information.