PololuPres_V3.pdf is not a document that we created. Could you provide a link to it? It looks like you are trying to set the current limit of your A4988. If so, your diagram looks fine, assuming your multimeter is setup correctly.
All grounds are internally connected on the board so either ground will work for your connections. However, you should keep in mind that all of the pins on the left hand side are logic pins so you should generally be thinking of the signals connected to them in terms of logic-level voltages (e.g. trying to drive them high by connecting them to 12V would destroy the board).
Lastly, connecting power backwards is very likely to permanently damage the board.