These two articles give good information. The jail piece says that transgender individuals will be held in the women's jail BUT in a section reserved for transgender individuals (up to 24 people).
With regard to addressing individuals, the department encourages officers to go with how the individual presents him/herself (clothing, language, demeanor) and bans frisking for the sole purpose of determining anatomical sex.
http://www.mercurynews.com/breaking-...stops-searches
http://latimesblogs.latimes.com/lano...ansgender.html