It says the VSs are outputs for the usb power (5 volts). How can I use a DMM volt meter to read the output voltage on the VS?
Connect the +DMM to VS and the -DMM GND. To guarantee a good reading, you need to make a secure connection with the screw-terminals clamped down. Just touching the screw heads usually does not work, especially if the screws are loose.
And then if I wanted to read the voltage in off of another battery (two batteries at the same time), could I hook the +battery up to AIN1 and the -battery up to the same GND as before?
It depends whether the batteries are referred to each other.
Example: If you just have 2 batteries sitting on your desk not connecting to anything or each other, they are floating. Since they are floating, you can connect both -battery signals to U6 GND, and thus you are defining both -battery terminals to be at the same potential.
Example: If the batteries are connected in parallel, then both -battery terminals are already connected together, and you just need one connection from either to U6 GND.
Example: If the batteries are connected in series, then the -battery terminals are referred to each other but are not the same. Say you have 2x 9V batteries connected in series ... that means one of the -battery terminals is at a potential 9 volts higher than the other. A way to handle this would be to make a connection from between the 2 batteries to U6 GND. Then connect the lower -battery terminal to AIN0 and measure about -9 volts, and connect the upper +battery terminal to AIN1 and measure about +9 volts. With more batteries you might get into using differential inputs to measure the voltage across each cell, but still need to consider the voltage on each AINx terminal compared to GND.