Merging Equivalent Concepts in OWL

I got a great viewer question on my ontology stitching video. I answer the question, hopefully giving some insight along the way.

Here's the question from Faiza:

"If we have 2 ontologies with same classes (some ontologies may have additional classes/concepts but overall the concepts are same in all the ontologies), these ontologies may have instances that are similar semantically but written differently. For example, Diabetes_Mellitus in Ontology A and Diabetes in Ontology B. How can we compare these two instances and maintain the aliases? Is it better to create an upper ontology, or should we merge these graphs? And what if we have to trace individual instances back to the original ontology they came from?"