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:
It does not contain schema comparison results or object DDL. When the file is opened, schemas are recompared. If target or source can not be found, the New Schema Comparison dialog box opens, where you should set source or target options.
When opening the document where a schema and a project are compared, the project should be opened.