My story-writing thoughtprocesses can be summed up as 'Who is doing what and will they successfully do it?'
Once I have that question answered, it's all about filling in the timeline.
Slight spoiler involving EverWander, but it's not really crucial... Sara and Acied won't make it back to Kaetir. For the sake of EverWander, they stay and adapt to life there. In this case, the end goal for them isn't 'Will they go back', but rather 'Will they survive in Gensokyo'. Trying to find a way back is just another event in the series of events on that timeline that they'll have to experience, and though they fail it, their over-all objective - survive - isn't affected by it. The entire story continues on because of it, but it's not the point behind the story.
In essence, that means that you come up with the exact end-goal you want for the story, then come up with the important plot details, the slightly-less important plot details, and then some of the minutiae between to fill in the gaps. Once you have a chain of plot points going and set in stone, you can essentially 'make up' the little stuff between the bits.
Another EverWander example - when Sara leaves the Voile after Acied shows off his new spellcard - I'd always planned for her to come across Yuka and Haru, as a way of cementing Everlasting Wanderers to the Reborn in Gensokyo storyline. I never thought of having Sara psychically blind Acied, causing him to ask Meiling for aid - which will in the future make Acied feel indebted to Meiling, another very minor plot point - and I didn't really think to use Tenshi as the bridge between Sara and Yuka.
Acied feeling like he owes one to Meiling gives me a potential tool for later that I can easily toss aside. In-story, it's a minor favor that can be repaid with something as simple as bringing her a drink while she's on guard duty sometime, or it could be that Meiling (somehow) is in need of aid that Acied is qualified to offer. I haven't spent any time thinking of a scenario that that could apply to, so that's liable not to happen.
Tenshi, on the other hand, was a necessary addition. If Sara had vandalized the sunflowers herself, Yuka would've directed her hostility towards her. There would be no way I could reasonably get Sara through that kind of situation - she wouldn't be able to beat Yuka without coming across as a Mary Sue, especially since she'd only fired her first danmaku shots the day before, and if she'd gotten herself beaten to a pulp at Yuka's hands, she'd never have a convincing reason to be on pleasant terms with Yuka - which is another potential avenue I could take the story in, and I do in fact have a minor plot arc in mind that makes use of that fact.
In my case, because of the way the gears in my head grind together, story-writing is all about plotting and planning, then filling in the cracks. The best advice I can give, though, is just try to finish a story all the way through, and then read it yourself. See what parts of your writing style you like, what you think needs improvement. See if you like the flow of your story.
Part of the reason I believe Everlasting Wanderers doesn't have a large following is because I spend too much time establishing the characters, and the first few chapters drag on. It could probably use a bit of balancing between action and exposition. See if you can find a happy medium with your works.