Hi!
It depends on which fandom is the primary/main setting for your fiction. If it's set in the Naruto 'verse and uses Harry Potter characters, it really belongs in Naruto, with a disclaimer for both fandoms. (I'm using random examples, of course!)
Most of the subdomains have a sub-category for crossovers, which would be the secondary level you can select when you're posting the fiction.
I hope this helps!