When I log Total Time (or Duration in some logbooks) I add up everything, including sim time. I also do my logbook pro program this way as well -- HOWEVER -- I always subtract sim time, etc from my total time when asked what my total time is. So you can log your time anyway you want as long as it makes sense to you and you can explain it to whoever may be looking at it.

There are no standard conventions on how to log your time. I only do it the way I do it because thats how a sim instructor logged my time back in 1995. Its too much trouble to go back and fix it and I'm used to it. It works for me and I have no problems in interviews or explaining it to anyone. So go with how you want to do it.