How do you make sure you have the right voltage on the trimpots on an A4988 stepper driver?
I want to add some points and clarifications to the answer that @darthpixel already has given. Most information you need is in there, I want to give some more practical advice, since that is what I understand you're question is asking for. I'll start with some points on the more theoretical side, though:

notice that the Vref is not a voltage that is passed on to your motor. The described pipe analogy is very good, but the Vref is outside of this analogy. The reference voltage Vref is only used to set the current limit. This seems confusing, but has electronic reasons. One can understand the major (side-)benefit easily: Voltages are very easy to measure externally, because you connect your voltmeter in parallel. If you wouldd want to measure the current, you would need to get your ammeter in series with the circuit.
The stepsticks work by supplying the needed current for movement of the motor (current, because it works by creating magnetic fields), the voltage the stepstick supplies is 'just' supplied as high as needed to feed the desired current through your motor (determined by its resistivity/impedance). This just as an add-on.

Now to the practical side and the application of darthpixel's answer and the above:
You want to measure the reference voltage to limit the current that produces the torque, but also heats up the motor - let darthpixel's advice be your guide: if you can't touch it because it is too hot, then there is too much current, i.e. Vref is too high). To do so:

Set your multimeter to volts, range can be autorange or something bigger than 2V.
Connect one lead of your multimeter to the ground of your Prusa i3 controller board's power input (I use the screw that fastens the ground input of the RAMPS). The other lead goes directly to the center of the trimpot on the Stepstick. I took the best of my paint skills to create an image showing the process: 
Note the value you read (12V power has to be on)
Use an insulated screwdriver and turn the trimpot slightly.
Get a new reading by repeating the measurement process.
Repeat the whole process until you get the desired Vref.

Warning: While I've had no problems turning the trimpot while everything was switched on (with my DRV8825 drivers), you should switch the power supply off when doing so.
The described process allows only for a stepwise and rather slow setting of the Vref, but this is the easiest way I've found. I have read of people that use a crocodile clamp to attach the multimeter to the screwdriver for a readout while turning.
If you don't have any idea whether you need more or less current on the motor at the moment, check your resistors on the board and calculate the Vref you should need (see darthpixel's answer for the formula). I would however just do what darthpixel already suggested: figure out the trimpot position by ears and touch: klicking motor: go to higher Vref. Can't touch the motor for more than some seconds: go to lower Vref. It might be a lengthy process, but in the end you'd need to do it anyway to get the best out of the printer!