I know I've heard from those in the past that have used mind mapping software alongside Logos. I just recently tried it out and I love it. I'm using a free program called Freeplane to collect info about the atonement. My plan is to go through the NT and note all verses dealing with the death/burial/resurrection/atonement, categorize them according to the contribution they make to the subject, and then link those contributions to resources in Logos that address the link.
Freeplane is working pretty well but for those who use for pay programs what advantage do other programs have over whats available for free?