For both database connections, the comparison tool has a special window where you can specify and execute any SQL statements. You can copy the results of executing a statement onto the clipboard or export it into various formats like text, SQL, HTML, XML or Microsoft Excel. Placing the mouse cursor over the column header will show the type of data stored in this field.
Menu item "Load" allows you to read SQL script from external file.
There is a picture of local menu accessed by the right click inside the results window.