It seems that in general, this process is a bit Chaotic (pun intended)
From the interview with Dan Abnett we have a bit of a glimpse:
Question: You mentioned the conversations with the editor – what’s the commissioning process like these days? Do Black Library come to you to say “please, please, please write another Gaunt book”, or do you go to them with ideas…? How does that work?
Dan Abnett: It’s a little of both, and it’s always been a little of both I think. The initial contact with Games Workshop, a long time ago now, was ‘will you write this?’ and I would say yes, and do it, and then onto the next thing. It was mostly based on what they needed and when they needed it by, to begin with, but as I wrote more and more – and let’s face it I’ve written an awful lot – and the books would sell, they would be keen to take what I would want to write. I could be more selective, so I could say “I fancy writing this, is that alright?” They would say yes, so I could sort of digress into slightly less obvious territory. [...]
The editors rang me up one day and said “We want a short novel, and you’ve got a gap in your schedule – do you fancy writing the novel for us? It’s a Warhammer one, as you haven’t done a Warhammer one for a while.” So I said “Yeah alright, what shall I write it about?” I literally asked what I should write it about…they said “Hang on, we’ll call you back”. About five minutes later there was a phone call, and they said “We’ve just had a chat in the office…what about pirates?”
Obviously there are times, Horus Heresy being the most obvious example, where they specifically want me to work on something and put my effort into that, and when you’ve got series like Gaunt in particular, but also the Inquisitor books, they’ll want one of those on a regular basis just to keep those series ticking over. But at the same time if I say “I want to write Space Marines”, or “I want to go and do this…” they are open to those suggestions.
The Horus Heresy is a bit interesting example, since the authors must stick (more or less) to the existing canon:
It does feel different, various things have changed simply because you learn things as you go along. Initially the decision was made by Games Workshop that they wanted to publish Horus Heresy novels, which was very exciting. They summoned about…I guess it was seven or eight of us to Black Library Towers, they sat us down and said ‘this is what we want to do, you’re the guys who are going to write it. It’s not going to be one person writing it, it’s going to be a team effort, and we’ll work from there’.So from that point on we became a body, a sort of ‘band of brothers’ of writers who just got together on a regular basis to discuss what would happen next, and then plan out the schedule from there.
Authors can be asked to write about a specific topic or just come with an idea and sell it to GW. In the case of big story arcs (Horus Heresy, Dark Imperium, Warhammer End Times), a group of authors and GW meet together to discuss the story.
But what is canon and who decides what it is?
Well... you do.
There are two good answers that I can quote here:
[...]is the job of authors and games developers to illuminate and inspire, not to dictate. Perhaps you disagree with the portrayal of a certain faction, or a facet of their society doesn’t make sense in your version of the world. You may not like the answers presented, but in asking the question you can come up with a solution that matches your vision. As long as certain central themes and principles remain, you can pick and choose which parts you like and dislike.(Gav Thorpe author),
So if you don't like something, you can always say that it is a heretical text, imperial propaganda or xeno lies.
I think the real problem for me, and I speak for no other, is that the topic as a "big question" doesn't matter. It's all as true as everything else, and all just as false/half-remembered/sort-of-true. The answer you are seeking is "Yes and no" or perhaps "Sometimes". And for me, that's the end of it. [...]But is it all true? Yes and no. Even though some of it is plainly contradictory? Yes and no. Do we deliberately contradict, retell with differences? Yes we do. Is the newer the stuff the truer it is? Yes and no. In some cases is it true that the older stuff is the truest? Yes and no. Maybe and sometimes. Depends and it varies. It's a decaying universe without GPS and galaxy-wide communication, where precious facts are clung to long after they have been changed out of all recognition. Read A Canticle for Liebowitz by Walter M Miller, about monks toiling to hold onto facts in the aftermath of a nuclear war; that nails it for me. To attempt answer the initial question: What is GW's definition of canon? Perhaps we don't have one. Sometimes and maybe. Or perhaps we do and I'm not telling you. (Marc Gascoigne, BL general manager until 2008)"