The "Listen" stage of the process is all about spending time in the text. Do whatever you have to do to get into the text and hear its word for you and the church. Pray over the text, observe it in its context, find its tough and rough places, hear the part of it that you're not quite ready for, and keep pushing and digging until you've heard the word that needs to be preached. When you have, move on to the "Focus" stage.
This stage, as much as any other, may really be done best away from the computer. (This is a hard thing for a developer to admit!). Truthfully, this app is not primarily for exegesis, and there are a few reasons for that. First, I feel like it would overly blur the focus of the app. Secondly, there are great software tools for doing work in the text, like Accordance and Logos. And frankly, the third reason is the most significant—I just don't think the best ways to listen to the text are in front of the computer. I think exegesis and discernment happen best when I'm either alone with the text (walking, praying, chewing) or kicking it around with other people. I simply don't know how to code that.
Nonetheless, the Sermon Design App includes space for you to capture notes from your time with the text. Simply create a new note with the + button at the bottom of the table, and fill in the text in the open are as you wish. When you are ready for the "Write" stage, those notes will be available as you formulate the actual final wording of the sermon.
One way that this might be useful is by creating a note with the text for the sermon inside it, so that you can continue to refer to the text as your write or sort through and create other notes. Simply copy and paste the text into the note from another source, such as one of the apps mentioned above or from a web resource such as BibleGateway.com.