We have a Safe Word, but usually he can tell from my tone and I can tell from his tone or body movements (Doms sometimes need to stop, too) when something is too much.
Last night, he was getting too aggressive with the anal probe and I gently touched his hand.... nothing. So, I finally did have to say, "Not so hard." Then, I had to really let him know it was getting into "bad hurting territory." Not terrible bad territory, just it was at a weird angle and I wanted him to change it. He did and after that it was amazing.
We know each other really well, so usually he can tell from my tone when to slow down or stop. I guess last night he was really into it and I had to stress the Safe Word.