You guys should totally separate these two. As you get more lessons (and lessons for more difficult material), I think you'll find users wanting a hyperlinked Table of Contents for the lessons.
You should think of this website as a book with interactive excercises, rather than excerises with lessons in between.
Also have you thought of any gramatical exercises or excerises that force the user to see kanji/words used in context? For example, どうぞ is taught pretty early as "please/kindly", but a learner would have no idea you can hold open a door and say どうぞ in a kind of "after you"-like sense.