Estimated Material Cost is the cost field found on the Inventory Part and can be applied across or utilized by all cost sets.

Cost Set Estimated Material Cost is the cost associated with the Cost Set selected and can be different to the other cost sets and different to the system Estimated Material Cost.

When performing the Cost Calculation for a given cost set, you have to make a choice between the EMC or the CS-EMC for the calculation run.  You can also decide to update the EMC from the CS-EMC while doing the calculation or you can decide to keep them separate.  

It is an additional cost set lever used mainly by cost accounting when updating cost, whereas the Estimated Material Cost is intended to be accessible to Planners and Buyers when doing the setup for a new part and is typically set the same as the Primary Supplier’s List Price as a starting point.

Lots of flexibility how you use each according to your business needs.