I used to take notes electronically all the time and I ran into your problem in different classes. What I realised though, was that it was not a matter of speed, it was a matter of categorizing!
Allow me to explain.
You said you wish to take notes so you can sort them later and what not, that's a great idea and it worked great for me too! What I did for my equations though, was write them by hand on a notebook and (in the notes) refer to them as EQ1, EQ2, EQ3 etc... When I got home, I would review my notes and I would then type the equations in the notes!
This proved to be sufficiently fast if you have a notepad that you can fit on the desk with you (if you have a full-sized laptop, maybe try a smaller notebook).
I ran into this problem when I took a CS class that was making use of flow charts, I certainly didn't want to draw the damned things with a tablet, I simply drew them by hand, referred them in the notes as fig1, fig2 etc, and when I got home I would (sometimes) scan the drawings and paste them in!
I know this isn't a suggestion for software, but maybe it can help you with your notes in the mean time.