You need multiple labor setups but multiple master estimates can be difficult to keep synchronized. A better solution is to create one master with the labor, equipment, crews and default settings and then copy in labor rates from a Labor Master for each estimate that has different labor rates from the default master. Same labor codes will exist across all the labor masters but each labor master can have different rates, taxes and fringes. Since the labor codes are the same only one crew setup is required. A labor master is like any other master estimate but you are only going to keep labor rates in it.  This is a graphic on how this works.

To create a Labor Master start with the source estimate being a blank master and then customize the labor as shown below.

Now to create an estimate with prevailing wages for example just use the customize button when creating a new estimate. I did a short video that shows the workflow for creating a new estimate utilizing different labor rates (in this case prevailing wage) from the default Master Estimate .