So, I make foldable templates in the SMART Notebook software to write on top of. This isn't foolproof. I often have students take notes in the wrong place, but I think that's a result of their not paying attention. Because usually 95% of the class will do it right...
Here's an example of what my SMART Board notes look like and what the foldable my students end up making looks like. I write everything every class period. This can get a bit old, but I find myself tweaking my wording throughout the day. I take what didn't work first hour and try to make it better third and fifth hour. I teach 3 classes of Algebra 1 and 2 classes of Algebra 2, so I never have to write the same thing more than 3 times. There are some things that I type out in advance for my students. And, there are some days when I think some notes will take 3 minutes to write. When they take 10 minutes in reality, I usually end up typing them out for the rest of my classes and simply have them glue them in. Timing activities can be really tricky with interactive notebooks. I've found that giving my students a specific amount of time to do a task (via a timer) can be a big help! I wrote more about using a timer in class here.
As you can see, I try to incorporate lots of color-coding. Doing this is pretty easy on the SMART Board. Plus, if a student was absent, I can always pull up the previous day's notes on the SMART Board for them.
The notes look super messy once we get done, but my students don't seem to have too much trouble following along with what's new on the page. Though, they do take every opportunity they can get to criticize my SMART Board handwriting...