Most of the popular syllabi have forms for doing this. Jeppesen makes some
very nice folders that allow you to track and grade the progress of each
student. Cessna Pilot Center software is kind of cheesy (it is written in
Toolbook and is better than the previous version which was written in
Paradox -- I suppose the next version will be written in Clipper, or maybe
FORTH or Smalltalk or even a Microsoft Word macro). Nevertheless, it mostly
works (emphasis on 'mostly') and customer support is better than average.

One would think that at the very least the software would allow you to
assign a grade to each lesson as required by VA. But it doesn't.

In fact, it would be very nice to have software that does all the VA
paperwork for you.

Or software that keeps track of your progress towards Gold Seal instructor.