The lab course (digital electronics) that I am teaching right now uses a checkpoint system where students call me over to show me that their circuit is working as desired or that they have sorted out the answer to some conceptual or application question. Quite often, the raison d’etre of a given checkpoint is to provide an excuse for me to have a specific conversation with each group of students or to provide a time for telling. And sometimes the checkpoints evolve into these things as I realize that there is a key idea that they are having trouble with.
In terms of keeping good notes, what is happening is that I want to keep notes on the conversations I want to have with the students with respect to each checkpoint, and I also want to keep notes on revisions for the labs. My labs are written using Word 2010 (keep your judgements to yourself, I have my reasons). My solution, which I just sorted out this morning, is that I will use the (balloon) comments in Word to keep track of the revisions that I want to make and I will use my new Word kung-fu to make instructor notes using hidden text (which I can choose to globally show or hide) so that I always have a single document that I can give to students (sans instructor notes) but also use myself (with instructor notes).
To make a student version of my lab, I go back to File >> Options and click the Hidden Text button and then export the document to PDF.