So in the project, I'm doing with my friend, we've had a lot of discussions about tone, and what we want the project to feel like, and then how to best get across that tone with the visuals and the writing. Ideally, the writing and the art complement each other to such an extent that neither could be removed or changed without impacting the final quality. "Total Artwork". It helps that we've known each other for a long time, and have a clearish understanding of each other's influences, and what we both like/don't like in media. I understand his goals, and he understands mine.
As an example, one of the big things we discussed was how to visualize the magic in the story, I asked them lots and lots of questions about how the magic worked, how it felt, what it does. "Does it hurt? Can they do this? Would doing XYZ make things more potent? How difficult is it to do something simple? Is this like Harry Potter or like Star Wars?" etc. Once I had a clear picture in my head of how magic worked in the story, I proceded to doing concept sketches, drawings of the characters casting the magic, designs for magical effects, etc. And I would show those designs to my friend and get feedback, he would say things like "This should be more forcefull, make this look more painful, make that bigger, this is very good so don't change a thing" etc, and I would go back and adapt my designs based on their feedback until we reached a point where both of us were satisfied, which sometimes meant me putting my foot down. "Hey no, magical swords are really dumb and doesn't fit with the tone we're going for at all. We're not doing that.", "What about just a regular sword that they use like a wand?", "Ehh, maybe? If I change their character design so that fits better, okay yeah that's pretty cool."
^That is effectively our process. It's a discussion.