the 3.3V and GND IO are direct connections to the CPU power rails. They can be used to supply or source power.
+5V IO is an input only intended as a way to power the on board regulator without needing the USB connected. There is no 5V output available when running from USB unless you make hardware changes.
When running from USB or from the +5 IO pin the 3.3V IO will be 3.3V (minus a diode drop of between 0.1 and 0.2).
When running from the battery terminals the 3.3V IO will be the battery voltage (again minus a diode drop of between 0.1 and 0.2)
All grounds (USB,battery and IO) are tied together.