For one thing, I try not to read many in-progress fanfics. I’ve been burned so many times by starting to read a story and finding out that it’s abandoned that I rarely start reading new incomplete stories – at least with an expectation of them being finished. That means I don’t have to remember so many things at once – when I finish reading one fanfiction, I can forget it. Even if it’s incomplete, I usually don’t try to check back on it unless it has a fast update schedule – I leave it for later, knowing I’ll eventually look at my Favorites list again and read the newly-finished stories.

I also think of the stories in terms of a fictional multiverse, like the ones in Dimension Hopping for Beginners and the Stormseeker series (both recommended). I like seeing the different viewpoints on and versions of a universe. So that might be a way for you to tie all of the stories together – think of them as offshoots of canon, usually sharing little else.

I also have a personal rule that whenever I finish reading a big story that could take some digesting, I shouldn’t read any more fanfiction (from any fandom) until the next day. This rule is mainly to maximize what I get out of the story and prevent mindless, time-wasting reading. But it also lessens my confusing the stories with each other – it still happens, but only sometimes when I read two big stories on successive days.