The video guide above me is amazing and I used it to get most of my notes, but I thought I should clear some things ups:
If you do the last mission before collecting them you have to restart a new game and all progress will be lost. The progress bar in achievements will stay the same until you exceed the amount you had.
You do not require any more energy cores than the first few required missions give you. This helps if you are silly like me and do the last mission without collecting them
If you died shortly after collecting a note it does not count, I died directly after picking up a note and it or the one before did not count. If you died go back and double check you have them.