The first is to do a "second pour" or "repour". To do this, reheat your wax to 5 or 10 degrees higher than the original pouring temperature. When the wax is at the desired temperature, carefully and slowly pour a bit of wax into the top of each of the molds, "topping them off." Pour to the very top of the cup.
The other way (and the way that I prefer) is to use a heat gun to "top off the candles". I hear you say, "Hey, that's a bit tricky to do in paper cups with drinking straws as wick pins!" Yes...you're right. And not everyone has a heat gun in their arsenal of candle making tools. But if you do, pull the straws off of the wicks, and just be gentle with the heat. Wax will melt at a much lower temperature than paper will burn. Slowly melt the top of the candle with the heat gun until the top is completely melted and flat.
Let the candle cool and start cleaning up.
If you've measured correctly, you should not have very much wax left over. (Put a note in your notebook if your measurements were off!) Either pour the remaining wax into a coffee can, or, if there is just a little bit, carefully wipe out the remaining wax with a paper towel.