In general, it's a bit of a toss-up. The strength of Manga Goku and Anime Goku can vary depending on the specific arcs and battles. Sometimes, it might seem like one is stronger in a particular situation, but that could change in another.
One possible storyline could be that Naruto is somehow transported to Goku Black's universe. There, he has to face Goku Black who sees him as an intruder. Naruto would have to quickly learn about Goku Black's powers and find a way to fight back using his ninja skills. Another storyline could be that a powerful villain creates a rift between their two universes and pits them against each other. They start off as enemies but then realize they are being manipulated and team up to fight the real villain.
There could be a storyline where Beerus, out of boredom, decides to train Goku Black instead of fighting him. But Goku Black misinterprets this as a sign of weakness and attacks Beerus. This could lead to a battle where Beerus has to hold back at first to avoid killing Goku Black, but as the fight progresses, he realizes he has to use his full power to subdue him.
Goku Black could start as a power - hungry villain in an RWBY fanfic. But as the story unfolds, he might have a change of heart. Maybe he sees the value in the teamwork and friendship of the RWBY characters and decides to turn against his original evil intentions.
Start by showing his initial goals and motives clearly. For example, if his goal is to conquer a certain planet, show his determination and the lengths he will go to achieve it.