Not Filemaker Specific, but I picked up a copy of "Case*Method Entity Relationship Modelling" recently. Older book, but really good for techiniques to model your database, proper relationship techniques, normalization etc etc. Basically all the architectural framework, questions and analyzing user needs BEFORE you even touch the database application. Written by a guy who worked for Oracle for many years.
I also have FileMakerPro9 the Missing Manual, good book, but I was/am in your shoes in that I really need to grab the basics and structure concepts first before I dive into "database mode". That was my problem, and thanks to some very helpful people here (and now this book!) I hope to get a better handle on data modeling and design.