I've always kept a paper chart since that's what I learned on (we used FAM in order to TTA). Now I use TCOYF.com and Fertilityfriend.com for 2nd and 3rd opinions. In my opinion, learning to chart on paper and seeing if those 2 apps agree with you is a great way to really pay attention to your symptoms. Plus paper is so transportable. (I know you can take screen prints and print off your FF charts, but paper is easy.)
So, I recommend paper charting since it's pretty easy to do. I made my own template in Excel if you want a copy of it, just PM me.