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Feel free to keep replying to this thread in order to get the help you need, but please keep that fact in mind for any future questions you might have.
That "missing manual" will likely help you out quite a bit. ;-)
In filemaker, you can establish any number of relationships that link a record in one table to one or more records in another table. It can be a table in the same file or a table in separate files. It can even be the same table (called a self join.)
Given that you are new to FileMaker, you may find it much simpler to set this all up in the same file.
Now to more specific suggestions:
Much depends one what you've defined so far. If you have a field in the Main Databaseset up as an auto-entered serial number, you have a field that will unqiuely identify each main database record. You can then set up a relationship that links a record (think a row) in the syllabus database to one in the Main database.