Pinout
The AC coupled pins remove the DC component from your signals, and are meant mainly for audio purposes and dual-ended opamps. For general use, you will almost always want to use the DC-coupled pins, as they do not alter your signal in any way.
The duplicate oscilloscope pins are there for measuring resistance and capacitance on the multimeter. You do not need them otherwise.
The fuse bypass pins (to the immediate left of the USB connector on the diagram) are used for bypassing the fuse, if you need to, by shorting them together. The top pin, as seen on the image, is a 5V pin directly from the USB connector, and the bottom pin is the 5V output of the fuse.
The fuse is a PTC resettable fuse, with a maximum current of around 400 mA.