You do not need to log it towards Total time in Logbook Pro. You can just enter a 0 in duration and the SIM time in SIM. This will remove it from duration.
If you want to go one step further you can also create a seperate a/c type (e.g. B727 SIM) and still only log time in the SIM column.
I personally do not log any of my sim time in my total time.
If you have any question let me know. You can send me a PM or submit a help ticket at
Logbook Pro's help desk
Regards