Before comparing the content of two databases, xSQL Data Compare will analyze the schemas of both databases (or the selected tables). If you manually map the tables between the two databases, xSQL 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 - every table on one database is paired with a table (when possible) on the other database.
For each pair of tables to be compared xSQL Data Compare will first determine whether there is a predefined primary key in both tables in the pair - if it can't find one the pair will be marked as "Non-comparable". Note however that a "Non-Comparable" tag does not mean that you will not be able to compare them - xSQL Data Compare will allow you to define a common unique key as a combination of fields in each of the tables in the pair.