When writing the fanfiction, create a detailed plot. If you're having a Naruto character in the Gundam Seed world, think about how they would react to the advanced technology. For instance, Naruto himself might be excited about the big robots but also try to find a way to use his ninja skills in that context. Also, pay attention to the character development. The experiences in the new world should change the character in some way.
First, you need to understand the core elements of both universes. For Gundam Seed, know about the different mobile suits, the political conflicts between the Earth Alliance and ZAFT. In Naruto, study the ninja techniques, the chakra system and the relationships between the villages. Then, find a unique concept to combine them. It could be a character from Naruto ending up in the Gundam Seed world or vice versa.
Don't forget about the dialogue. Make it true to the characters. In a Gundam Seed and Naruto fanfiction, if Kira Yamato from Gundam Seed is talking to Sasuke from Naruto, their different personalities should be reflected in their speech. Kira might be more hesitant and morally conflicted, while Sasuke would be more driven and focused on his goals. Also, use vivid descriptions to bring the combined world to life, whether it's the desolate battlefields of Gundam Seed or the lush forests of Naruto.