As for the rest, scripts that relates one table to the other its all made manualy or is that a feature of the bench too ?
MySQL Workbench is simply a GUI tool for working with MySQL databases and the features that are built in to MySQL.
Although you can just create your own relationships through your external PHP or Livecode scripts, there are some built-in features in MySQL that are nice to use (which Workbench or other tools can help you manage)
For example:
Foreign Keys, which will help keep data consistent (amongst other things).
Another thing to look into is
Views, which can combine fields from various tables to create a sort of "virtual" table...good for simplifying queries (amongst other things)
so, in short: you can just manually access tables create relationships from your scripts, but using some of the built-in features of MySQL and having a mapped out database structure can help a lot in keeping your data organized, consistent, and easy to access.