My log book has a column labelled "sim". I log all of my simulator time there (regardless of what I did in the sim). That column, however, is not included in my Total Time.
In the past, training that I did in the actual aircraft was logged in the "dual" column, and that was included in the Total Time.
Basically I keep track of how much time I have in the sim (I include the sim ID in the entry) but I don't include it in my total flight time.