The two diagrams differ mainly in that the first one has the meter's power supply isolated from the supply for the thing being metered, while the second the meter and the thing share the power supply. Since you don't need an isolated power supply, you'd presumably use the second diagram with the controller and the motor.
The + and PW+ wires go to positive from the battery (presumably via an appropriate fuse).
The COM wire should go to the more negative side of the shunt, which for your use would be the chassis ground side, assuming you're putting it as usual between the chassis ground and the negative battery lead.
The IN+ wire should go to the other side of the shunt, i.e. the battery side.
If for some strange reason the amps reading shows the wrong direction, swap the two leads from the shunt.
There's a very slight chance that using an isolated DC-DC converter for the power supply (which would be connected to the power supply + and - connection) that you might actually be able to get a current reading in both directions. You could test that by hooking it up to a 9V battery or similar, I suppose, and seeing what it does. Most likely it won't show negative current.