One of the great fanfictions might be those that explore their unique relationship within the horror - filled world of FNAF SL. It could be about how they interact during the 'nightshifts' in the game. Maybe there's a fanfic where they team up against some common threat in the animatronic world.
You can start by looking on fanfiction websites like Archive of Our Own (AO3). It has a large collection of FNAF - related fanfictions, and you're likely to find some good ones about Funtime Freddy and Funtime Foxy there. Just use the search function and type in their names.
The animatronics themselves can be considered main characters in a way. Freddy Fazbear, Bonnie the Bunny, Chica the Chicken and Foxy the Pirate Fox play significant roles. They are the sources of horror, with their own distinct personalities (although they are haunted and menacing) in the stories. For example, Freddy is often depicted as the leader among them, and his appearance is always a sign of great danger.
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The main characters usually include the night guards. They are the ones who have to endure the terrors of the haunted animatronics during their shifts at Freddy Fazbear's.
The main characters in the FNAF game story are the animatronics like Freddy Fazbear, Bonnie the Bunny, Chica the Chicken, and Foxy the Pirate Fox. There's also the night guard, who is the player's character and has to endure the nights in the haunted pizzeria. And then there are the children who are somehow related to the whole mystery, either as victims or as spirits that may be haunting the animatronics.
Well, there are the animatronics, but also the security guards. They play a crucial role as they are constantly in the middle of the action, trying to survive the nights in the pizzeria. And let's not forget the unseen force or entity that seems to be behind the hauntings of the animatronics. Each of these characters, in their own way, drive the story forward.