I struggled with this in the beginning too, for example, if you’re hiding in grass and a guard approaches, the window to take them out by assassination before they spot you is quite short. I manage to keep stealthy now by a lot of patience, and taking the time to mark all enemies with Senu (this becomes easier with time since his perception increases every time you synchronize a new spot).
Also - make sure you set traps at the fire braziers in case they actually spot you, this helps a lot as they blow up instead of calling reinforcements =)