You can save the Schema Comparison document (the one that opens after comparison to show comparison results) for the future usage. The saved file has the .scomp extension and stores schema comparison information, including:
Selected values for comparison options
It does not contain schema comparison results or object DDL. When the file is opened, schemas are recompared. If target or source schemas can not be found, the New Schema Comparison dialog appears, where you should set source or target options.
Saving Schema Comparison Document
Opening Schema Comparison Document