You can host multiple database files on FileMaker Server at the same time. You do not need to combine all of your tables into the same file though doing so can simplify certain details when it comes to managing your database system.
It is also possible to import tables and scripts from one file into another and then use copy and paste to replicate the original layout in the file into which you have imported the data. This is, however, something of a tedious process and requires paying careful attention to detail. (As well as manually recreating any value lists from the original file in the new "combined" file.)