In many ways it is easier and faster to build under a single hood in the current FileMaker 7 - 10 family. That being said a single hood database can also become a very slow, bogged down, crashing mess. When building your solution go back to the basics and do some forward planning. If your database has the potential to grow and grown big as well as have several modules added in the future then plan for the separated data model. Ideally you want your GUI (User Interface) in one file and all your data sets (tables) in other files depending on the load expected for the tables. In some cases it is best to even separate the interface structure but is only necessary when you have a large base of users in the module or interface in question.