You'll struggle to find any senior referees who stop their watch for all but the most serious of stoppages, and generally added time is "guesstimated". 30 seconds for a sub, 30 seconds for a goal, keep a mental note for injuries, time wasting, etc. Often with 4th officials the referee will ask him to keep a stoppages log and use that to advise the correct added time, and also use that log to justify the added time should either team complain.
Whilst not technically right I'm usually wary of adding any added time if the game is a cricket score. Of course if one teams needs the goal difference then it is different, but generally neither team wants a second over the 90. Twice I've observed referees who had good games and then had major incidents that cost them inside stoppage time that they didn't need to add. One team is frustrated, the other often starts showboating, it really is a recipe for disaster.