Thank you so much for the kind compliments!
Harem Hotel is my first try at just about everything you see and experience in game, so I was very much learning as I went. The only prior experience I had was through running a D&D campaign. It gave me plenty of experience allowing characters their own agency. But everything will come to you as you try and fail - it's just a part of the process. Feedback and criticism is also vital.
One thing experience with D&D also helped me with was writing story on the fly. Creating characters instantly with very little to go on. The method I applied to give any random NPC life is what I call the "That damn neighbor" method. It's perfect for small talk and can even lead to random people becoming fully fledged characters. The gist of it is, no conversation is ever only transactional, it should always include something personal, even if it's something random like "That damn neighbor keeps making noise." Considering context like, maybe the person saying that is a shopkeep, and the person making noise turns out to be a cultist, you suddenly have a whole storyline from an innocuous line.
As a beginner, it's almost impossible to see the hidden structures of a story. As a professional, every story becomes predictable because you can finally see that invisible structure. Like with all things, it is a skill. Talent is only Ambition + Effort + Time. I highly recommend that you digest a lot of stories so you can start to pick up on those invisible structures. Such as narrative archetypes like The Heroes Journey, Rags to Riches, The Odyssey, etc. Those aren't books, but archetypes. Harem Hotel is an Odyssey with a Rags to Riches story. This means you leave your home for a grand adventure, and start poor/powerless and gain wealth/power by the end. So you can see how knowing these things can tell you a lot about where the story is heading. But this is just one aspect of writing that you will pick up as you immerse yourself in your work and like-minded people. Practice makes perfect though, so start now. Even if it's bad, just start now. Nobody ever likes their first step but it's necessary to start walking. And nobody remembers the first step anyway.
Your workflow is personal to your life, so don't follow what I or anyone else does for that matter. You should do what works best for you, and that will change with the ebbs and flows of time, but you can learn a lot from seeing others work too.
So my workflow is that I am not sure what's going to happen next! And that keeps things interesting for me in the story. I have a direction of course, but each event is usually planned after the last one was finished every time. (Spontaneous writing I learned from D&D). So I first start an update by planning, usually just the story beats, a beginning, climax, and conclusion. I ask myself "Why does this need to happen?" "What is learned, or what is fun?" and "How does this get us closer to our goal?". Then I move on to "Based on that, what needs to happen, and how will it happen?". Then, if there is something on my mind at the moment, I will write down dialogue. That's the rough draft finished.
After finishing my drafts, development is ready to begin. This is when I usually start by first creating any sets the story will take place in. Once it's ready, I create all the visuals and the dialogue at the same time. I very much let a character's personality drive the narrative of the scene I put them in, so it's not very possible to write their reaction before it happens, if that makes sense, which I think is a key to making any character feel alive. They are actually reacting in real time, like players in a D&D campaign, I just happen to be the dungeon master and playing my own characters at the same time.