Tips for Good Multi Crossover Fanfiction

Know your characters
Really understand their motivations, aggravations, and how they would interact with characters that aren't from their series. Try and peg their personality and then figure out their relationship to everyone else in the story. Like you they will get along with, who they won't, and be able to explain why. Even if you don't mention the reasons in the story it's good for you to have that background knowledge to be able to fuel their actions in the story.

Pick a setting that will make sense and accommodate all of the characters.
A good crossover (As you know i'm sure) should be able to make sense. And if the story takes place all over Earth, Mars, and beyond it will be hard for readers to grasp a sense of reality in your story.

Ease in to things.
It's good to outline the timeline of the story because it helps give you a sense of how fast you should pace events in the story. I wouldn't try and rush into introducing ever character at once, or even within the first couple paragraphs. It's better to introduce a couple at a time and space things out a little, or else the reader might get confused (If they aren't already with the character) on who is who and why they are there. ...I guess what i'm trying to say is create a small development with each character before you bring on another one. Just establish a connection with the reader, by pointing out what the character is wearing, or maybe they way the look, and are holding themselves.

Lastly don't give up.
It's tough to get a good handle on writing a multi-crossover because it requires putting certain personalities and abilities (if any) together, that don't normally mesh like that. I think if you keep writing and working on it everything will fall into place. You just need to outline a plot and roll with it!
Good luck! Send me an inbox once you make some progress, I'd like to read it. I hope this was able to help somewhat! (Sorry it was a bit long)