I put together a quick demo of one way this could work here 
http://inmysocks.tiddlyspot.com/#Note%20Taking%20Test
It doesn't have any searching ability or anything yet, but the notes and 
questions have fields indicating the class and date they are from, so 
searching etc. can be added later.

The problem I am running into is writing the notes and questions. Normally 
for things like this I use a temporary tiddler for editing and then when 
the new tiddler is created the content is copied to it, but in this case I 
want the notes and questions to be updated as you type.
Unfortunately I am displaying them using a list widget and a template that 
contains <$edit-text tiddler=<<currentTiddler>>/>, I expected this to work 
because the open tiddler wasn't the one being edited, but it appears that 
the tiddlers being transcluded using the list and template are being 
treated as if they are being edited directly and the problem of the 
tiddlers refreshing on every keystroke is happening, so typing notes isn't 
really possible.

I didn't expect this problem, and I can't think of anything I can do to fix 
this that doesn't require some sort of 'save notes' button. The reason I 
don't just have a single sheet for editing notes and questions for each day 
is that I would like to allow separate notes for separate topics during a 
single class to allow them to be easier to search for, and if I continue 
making this I will probably use the same interface for viewing notes so 
that you can easily edit them later if you want.

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