In a separate thread, Daniel asked how we use OneNote along with Logos. I gave part of the answer in another thread - in response to Bob Pritchett's request for details on how we use Notes. I will probably give more details than you need -- but here goes.
My use of OneNote is probably clumbsy - but it what is working for me now. A bit of background may allow you to understand my interest. As a part time pastor (otherwise on disability), I do not have a long history of sermon preparation. My seminary (TEDS) was completed some 30 years ago and I served as a pastor for five years after seminary graduation. God then took me into Post-Secondary teaching for 24 years. I completed a master's degree in Computer Science Education and (later) in Community Counseling. The latter degree was the first part of my bringing my ministerial credentials up to date. I also completed three units of CPE in three (two very) different settings. Seven years ago I began to serve a small United Methodist Church, was ordained by The Wesleyan Church. I was diagnosed with MS in 2002 and earned the title of "totally disabled" in June 2007. I continue to serve the Garland United Methodist Church in Brockport, NY, 12 hours a week. We have two services - a traditional service in the morning and a service at a senior living complex just south of town. Between sermon preparation (including three office hours per week), two services, and a small amount of visitation, my 12 hours goes pretty quick.
I first was introduced to OneNote on a tablet PC while teaching - and brought it with me to the ministry. I start the week by coming down from Sunday and beginning to think about the passage (normally) or topic (a series I am currently working on). On Wednesday night I will select my hymns for Sunday - it is early, since the sermon is not completed, but the pianist needs the songs so she can practice. Also on Wednesday and on Thursday (when I have my only office hours) I begin to gather material. If I am doing a passage I will create a dynamic outline of the passage in OneNote. If I am doing a topic, I will read and outline my major source for the series.
I then make my way (only scanning material at this point) through Logos identifying helpful books and authors. I will "Print to OneNote" those items I find particularly helpful. I also create a link in OneNote back to the source material. In OneNote, I will format material so that if fills about 1/2 of the page. As I really read the material in OneNote, I will hightlight important concepts and make notes on the other half of the page. Being that I use a Tablet PC, notes are sometimes handwritten, sometimes typed. Occassionally, I will draw a picture to help me understand/remember a concept better. If my preparation takes me to a webpage, I can follow the same procedure there (print and take notes in OneNote). Since I am a tactal learner, all this drawing, highlighting, and writing helps cements ideas in my head. (Even in grad school, I would outline my textbooks by hand - a review of my handwritten notes got me ready for my exams 
. There were some fellow students that hated me for the ease at which I prepared for my exams.)
I will have one tab for each sermon series, one major page for each sermon, and one minor page for each resource that I printed into OneNote. I would occassionally have an extra minor page for my own thoughts - those that are not connected to any particular resource.
As I write my sermon, I will continue to review the material I prepared in OneNote. If I borrow an idea from an author, I can go back to the source and add a valid endnote to my sermon. By Saturday (sometime) I have a sermon ready - and move into Sunday.
I hope that gives you some idea on how I use Logos - feel free to ask for more details. I would also, like Daniel, like to know how others are using OneNote. I did see a template at some point on the NewsGroups from a user which showed how to use OneNote to support exegesis. I have also used a couple of borrowed templates from MS Word to support exegises - expecially if I am studying a passage.
Blessings,
Floyd
