I've made an entry with a statement in the Remarks about fixing a problem I found. Usually my SE/ME times didnt add up to my TT or something obvious like that.

There is no official way of doing it. Everyone has their own preference. Some folks say never use pen to help correct mistakes. I whole-heartidly disagree with this as most likely you won't make mistakes, and you don't run the risk of things being goofed up. Other than that it's all good.