As others have said, there are really 3 different places to put the shunt (3 correct places) in the schematic.
As in the Dynon manual, one is between the battery and the aircraft load and alternator. Basically, this is giving a +60 to -60 Amp reading. When the engine is off or the alternator is off with the plane running, this should show a negative reading, showing that the battery is seeing a drain. When the engine and alternator are on, this will initially show a high positive reading as the battery charges back up, and will ultimately show very close to zero during a flight as the alternator will be putting out what the aircraft load is using, with the battery fully charged and basically just sitting there and stabilizing everything. The drawback in this setup is that you don't know what your bus is using (you can calculate, but you don't really know), which makes it harder to load shed if/when your alternator fails. I know that Wheeling Strobes (3 lights) uses 6-7A, the three Nav lights use around 6A, and so on. If I turn on the Nav logs and one is burned out, this amperage setup won't tell me anything.
The second place is between the alternator and the aircraft load and battery. It will only give you a reading of 0 to 60A. It will just read what the alternator is putting out. If the voltage is good, then the alternator output is equal to he aircraft load, as in the first example when it reads close to zero. If the load exceeds what the alternator can put out, then the voltage will show lower than normal as the battery makes up for the difference. If you ever get a negative reading in this setup, then you are wired backwards. As you increase aircraft load, the negative reading should become increasingly negative. If you turn on lights and pitot heat, it should become increasingly negative. If this is the case, switch the two sense wires and it should flip. The benefit of this amperage format is that it tells you what your alternator has to put out to keep your battery charged, so if a Nav lift is burned out, it will only show and increase of 4A instead of 6A when I turn the Nav lights on.
The third place is between the aircraft load and the battery and alternator. This is not as common in my experience, although it really gives you a more accurate and stable reading of what you are using because the battery is not buffering the readings, as in the second example above. This will definitely help you determine if your Nav lights, strobe lights or landing lights are not working, because amperage will be showing exactly what you are using. This will also show negative is it is wired backwards, although showing negative is acceptable if you want to think of it as a high amperage reading being bad in the case of an alternator failure.
With examples 2 and 3, voltage is more importante to indicate the healt of your electrical/charging system than in example 1. In fact, I personally would MUCH rather have a good voltage reading than an amperage reading at all.
What had not been mentioned is the possibility that you have a Hall Effect sensor. If so, it is a ring and has a wire passing through it instead of being a shunt that has a wire connected to each end. A Hall Wffect sensor is less accurate, but can be installed in any of the above ways. If it is reading backwards, you just need to disconnect the end of the cable it is reading, and flip the ring so it is pointing the other direction to get a positive reading.