How can I make sure my data is correct when preparing for mask-making?

Make sure your Criteria are correctly set (see following questions). You can double-check this by using the Masks dialog to make only the desired Layer(s) or Type(s) visible. Then if you do not see all the data required for the mask, you know you need to assign the missing Layers and/or Types of data to the Criterion. You can also export your data to another format and reimport it (using the GPE sample(s) provided). Then superimpose it over the original data, compare the differences, and correct any problems before the data is transferred to a mask.