One of my goals this year is to study the book of Ephesians in-depth (I'm beginning to think I'll need/want to continue the study beyond 2009). After having done some background reading on the author, recipients, and historical setting, as well as familiarizing myself with the epistle as a whole, I'm now at a place where I'm ready to examine actual paragraphs or units of thought.
One of the crucial steps in studying a portion of Scripture is analyzing the structure or flow of the text. A great way to do this is by creating a "sentence flow" schematic. It's a method for visualizing the flow of thought in your text by means of aligning, indenting, and subordinating the phrases/clauses in the text. I've found Gordon Fee's New Testament Exegesis: A Handbook for Students and Pastors to be very helpful on this topic. The chapter on structural analysis, with plenty of sentence flow examples, can be found on Google Book Search here.
A related method for examining the structure of a biblical text is called "arcing". BibleArc.com is the place to go on the web to learn about arcing. The site contains some great tutorials and even has tools to enable you to create, save, and share your own arcs with other users of the site.
I'll be sure to post links to more resources as I come across them.