The base case values are the initial cell values listed in the Base Case column of the Decision Variables panel in the OptQuest wizard. The base case values are important because the closer they are to the optimal value, the faster OptQuest might find the optimal solution. If the values are constraint-infeasible, they will be ignored.
For potentially large models with many decision variables, you might find it helpful to first run a deterministic optimization to search for good base case values. Then, use the results as your base case values and run a stochastic optimization. This technique, however, might not work well if you have objectives or requirements defined with other than central tendency statistics.