I want to compare a DDL and a design using File|Import|DDL File. I know my design is correct but the comparison always shows the DDL to be correct and suggests me to change the design. How to I tell the tool that my design is correct and I want to alter the database accordingly?

It is very simple. While importing the DDL select “Swap target model”

Now the comparison will show the design as the source (truth) and the DDL as the target (false). AND it will give you the ALTER DDLs to change the database. Simply press DDL Preview to get those ALTER scripts.