generally with SF you want to reapply it in the 1 to 3 sec window however if a boss jumps AE is far better as you need to have at least 15s of SF to be above AE potency. this stays consistant until lv 70 where TenChiJin starts to mess with SF timing where during opener SF would just drop off as you reapply it and later ones you have 6 secs left on SF timing and its better to reapply SF early than let it drop.

I am a nin main not the best (by far XD) but i hope might help you