http://iscoresports.com/

I would like a way to keep track of offensive and defensive coach visits. I'm not sure of all of the rules, but I know that after the coach visits the pitcher 3 times he/she must change pitchers.

You can add notes if you would like to track coach visits. They will appear in the pitch by pitch / play by play listing.

That's not really what I'm looking for since that information is only useful post-game.
I was hoping for something in the misc context which would say offensive or defensive visit. Then when the maximum visits have been reached the appropriate action would be taken.

There are too many different rules concerning coach visits for it to be useful to try and do something beyond notes. Some leagues limit number of visits in an inning, some are number of visits in a game, some will depend on whether it is a coach or the manager, sometimes it is limited by whether a new batter is up, etc.