It's important to begin with the end in mind. For the EstimatorFLEX tool, start by looking at how you have things configured in ProPricer CE.
For example. You may want to make some changes to your direct rate decks in Contractor Edition to make it easier for your writers to work in Estimator or you may want to ensure the naming convention you use for your rate tables makes it easier for your Pricers to find and attach to the correct, current one.