Hi again Samuel (@samuelshannons),
it is common to select the master/slave faces and create topological entities in the Simulation Designer (keeping in mind that the entity sets from the Mesh Creator and the Simulation Designer are not the same). Creating a new Mesh from the same model will keep the sets and you can still work with them.
In the Mesh Creator these Topological Entity Sets are useful to define Mesh Refinments or any other operation and is useful in general to improve the workflow like Invert Selections for relatively big CAD models etc.
If there is still something unclear just let me know.