Before comparing the content of two databases, IDERA SQL Data Compare will analyze the schemas of both databases (or the selected tables). If you manually map the tables between the two databases, SQL Data Compare will use that mapping as is and proceed with analyzing the pairs of tables. It you compare whole database it will first perform a automatic mapping of the tables based on their names (owner name + table name) - every table on one database is paired with a table (when possible) on the other database. Then, it proceeds to analyze the pairs of tables to map individual columns, determine the available comparison keys and choose a key that will be used to pair rows during the data compare.
During this preparation phase you will be able to customize the object mapping, include and exclude certain tables and certain columns within those tables, choose comparison keys and define data filters to compare only subsets of rows from certain tables.