You pose a very good question, one that I had myself when I first started. I was always a pen and paper guy in undergrad, so when I transitioned to iPad in my first year of med school I was optimistic about what to do. My advice is this: everyone learns differently, period. This won't be the first time nor the last time that we as future physicians will have to adapt to changes in our careers. Some people have used electronic notes all their careers, others are pen and paper. It will take time to find out what works best for you, but the learning curve is fast in the first week or two. For example, here is what I do:
Personally, I now love electronic notes via tablet and actually prefer it now over pen and paper. For me, this is what I did. I downloaded the notability app from the app store, an app which lets you download powerpoints and pdfs and you can annotate them directly, save your edited notes, and upload them to cloud servers such as google drive. In class, I download the lecture and follow the professor. If something the professor says that is very good for clarification or not on the slides I would write it down on the slides on my iPad. Then I will go back later that afternoon/evening and study my lectures for the day from my modified class slides. I like to backup my notes onto Google drive and study from my laptop for example. This is where the pen and paper comes in to play. After quickly determining the most high yield points from each lecture (most likely to be tested on) I will write those high yield points into a notebook so when I study on the weekends or before exams I will just have to study from my high yield notebook that I wrote myself (unless where visual pictures in the lecture are important, like anatomy, histology, or pathology where I will study back from the slides themselves). This way I keep up with the professors in class and still use pen and paper. I will admit at first it seems like it may take too long, but the first couple of weeks is transition for everyone.
Some people only take notes in a microsoft document format, others print everything out. Do what is best for you to pass the first time and excel to make your dreams come true. Whatever has worked best for you continue to do it, med school doesn't have the luxury of free time to learn many new methods of studying.