Could others out there share how you use Accordance in compiling and storing information as you study? User Notes or User Tools?
I find myself using a variety of software as well. I quite often use Personal Brain for working out my rough thoughts on a text and for making connections with other thoughts and ideas. Then I will compile more specific exegetical notes on texts in User Notes in Accordance. I use the reference lists sometimes, but I'm still getting used to that function of Accordance. For writing my sermon (or papers) I put the information into Pages. I also use Yep to compile my PDFs (I have a lot of them, as I try to stay as paperless as possible). In order to find all of this information, I'm finding that I have to make use of Spotlight, Yep, and Accordance, and Leopard's new coverflow and quicklook features. It all ends up being a bit messy, but I think that helps--I find things "by accident" and that leads me into new, creative ways of thinking about the text.
Remember, a bit of chaos is good--leads to more creativity. ;-)