It's very confusing in my opinion, but generally if the inputs of a SUT are labeled with resistance values, in the case of vintage Japanese SUTs, this usually meant that one should plug the phono leads into the pair of inputs with the label (in ohms) that most closely approximates the internal resistance of the cartridge. In the case of the SUT you are using, and because it is not a vintage Japanese creation, all bets are off, since no LOMC cartridge has an internal R in the 47 to 100 ohm range. Luckily for you, you can just contact the manufacturer, as Elliot already suggested. Why they don't just label the inputs according to the turns ratio obtained with that particular pair of inputs is beyond me, except perhaps they think audiophiles are too stupid to figure out what turns ratio does to impedance or what turns ratio would result in an appropriate voltage gain for the cartridge.
Possibly the 47 ohm inputs give an input impedance of 47 ohms with a 47K standard load at the input of the phono stage. But that would imply a turns ratio of 1:32, which is a lot of gain. For the 100 ohm inputs, you would have a 1:22 turns ratio. (In other words, for the cartridge to see a 100 ohm load using a 47K resistor on the secondaries, the turns ratio would be 1:22-ish, which is the square root of 470.) The load seen by the cartridge is equal to the load on the secondaries (47,000 ohms) divided by the square of the turns ratio (~22-squared = ~470).
Meantime, just use what sounds best.