When plotting and writing stories, I always start with the assumption that characters are bisexual until proven otherwise, which I suspect puts me apart from a lot of mainstream writers. Some of my characters do happen to be otherwise -- either gay or straight -- but that's an aspect of their personal make-up that either they've given a reasonable amount of thought to, or that is going to get challenged in the course of the story (particularly with regard to the straight characters for the latter) even if they don't change their attitudes much by the end of their journey through the plot.
Sometimes I worry that my bisexual characters' sexuality is going to be invisible, mirroring the real life phenomenon of bisexual invisibility, if the whole story is about their involvement in one relationship. Sometimes there are good reasons why they should mention past relationships that involved someone of a different gender to their partner in the story, but sometimes (especially in a short story or with minor characters), that's not so easy.
In the SF story I'm revising now, bisexuality as a behaviour more than as an identity, is pretty much assumed by the universe at large for other people, and it's those who are presumed to be asexual that are looked down on as outside the norm. I also have one female character who mentions her deceased female lover and their child, and another who is in a relationship with a woman, but who mentions wanting to visit her children and grandchildren again. In both cases I've left it open to reader interpretation as to the exact sexuality of the characters (my opinion is that one is almost exclusively attracted to women and the other is bisexual, but other people's interpretations may differ).
In the world of ebooks especially, I get the feeling that mixed-sex relationships with more than two participants, all sharing each other equally, are becoming more common, but that's not the way all bisexuals run their lives. My big question on that subject is whether a book has LGBT relevance if one or other partner in a primary m/f relationship identifies as bisexual, even if their same sex sexual relationships all occurred in the past relative to the story. Where would that book be 'shelved' if the some of focus is on the bisexual character negotiating an outwardly-seeming-heterosexual relationship while not wanting to lose hir ties to the bisexual community?
In contrast to bisexual characters, I've written one trans* character so far, and that's Stuart in 'The Monitors', published in the m/f anthology from Noble Romance Echoes of Possibilities.
Writing Stuart was a lot of fun. He's an outsider for reasons that mostly have nothing to do with his gender identity, he's an opinionated intellectual, and he's more than a bit insecure in his dealings with other people (for reasons that again are distinct from his gender identity). Basically I wanted to write a 'boy meets girl on an otherwise deserted spaceship' story with a twist. Not that Stuart's gender is the main twist, but writing how he viewed his body while also considering how other people might see it was a fun challenge. (Stuart has had some surgery, but is still saving up for the last of his operations. Being SF this means he will end up with fully-functioning anatomical equipment, although he'll still have to adopt the children he imagines bringing up one day.)
As for Stuart's love interest, Claire: I always viewed her as bisexual, but avoided bringing that into the story, because I didn't want readers interpreting her sexuality as the reason for her attraction to Stuart. Claire likes her men masculine, even if they are also slightly short and skinny, and she likes feminine women (my opinion, not stated explicitly in the text). So she's not attracted to Stuart because of the gender he was assigned at birth: she likes the gender he's chosen for himself, thank you very much.
As with bisexual characters, it's not always easy to know how to categorise a story where one character or other character is trans* in what appears to be a standard m/f relationship. On the one hand, it is a standard m/f relationship, but on the other there's always the worry of what other characters in the universe (or even some readers) might think if they realise 'after the fact' that this person isn't quite how they had initially assumed them to be. Transphobia is a very real worry, and so I feel that there needs to be some kind of niche there for my story to sit with others of a similar leaning, regardless of the gender combinations involved in the main relationship(s) in the story.
Incidentally, the Tiptree Awards committee are still after nominations for this years' award, so if you've read anything in the realms of SF&F that does interesting things with gender go over there and nominate it (as well as recommending the story to me here: I always need new stuff to read).
I'll be reposting this piece, with a few additions/tweaks over at Beth Wylde's group later, along with an excerpt from 'The Monitors'.