Whichever bathroom they feel most comfortable with I assume. ie, someone living and dressing as a woman, whether or not she is biologically male or female, will use the womens bathroom.
And someone who is transgendered would determine their sexual orientation in the same way that anyone else would. For most, that would mean based on whether they identify as male or female, not whether they are genetically or biologically male or female. For example, Person X may have been born physically male, but has been living as a woman. Person X identifies as female and is exclusively attracted to men, therefore is straight, not gay.
I've hardly had any sleep so I don't know if any of that made sense or not, I'm very tired...