It's all comes down to your preference then. I'm not sure why you went with individual scenes rather than plotting out the story first as that should make writing it a lot easier. Anyway, I guess I could point out disadvantages and advantages with the perspectives if you like.
Remember, descriptions are how your characters view something. Take these two sentences for example:
Sentence 1 said:
She had a shit-brown colored hair.
Sentence 2 said:
Her chestnut hair whipped in front of me, a wave of sweet strawberries entered my nostrils.
There's a stark contrast between the two sentences, yet they both describe the same person. In the first person, you can convey your opinions more into your descriptions. How the narrator sees it is also how the readers see it. This could also help with your qualm with integrating Emile's thoughts. Keep in mind that the first person narrative means you're diving into everything the narrator sees, feels, smells, etc. Descriptions make the narrator come alive in a sense. It helps tremendously with making them believable as well. The thoughts also develop the character, but I can't really help you other than trying to make easy transitions from whatever you're writing to thoughts back to action. I'd suggest reading a few books that utilize the first person. Even reading a single page could work wonders.
The omniscient narrative dives into everyone's thoughts and views every single action, meaning very little opinions are implemented while most of it is dedicated to describing a wide range of characters at the same time. Nothing is hidden from the narrative. I would say that descriptions identify with the characters you're identifying with. You can switch from view to view without being jarring to the readers. However, the characters aren't as big in this type of narrative.
I don't think you should be concerned about which one to use for a specific scene. When you're choosing a narrative, you have to consider your entire story. If your story is big on the main character and you want a deeper POV, then go with the first person narrative. But if you want to be able to jump from place to place, time to time, and character to character, then you would probably want to use the omniscient. Because you're writing an original trainer fic, you'd probably want to use the first person as the story revolves more around the character and how he interacts with the world rather than looking at different events that happen across the region. And don't worry if you don't feel comfortable writing in that perspective. If you continue to practice, you should be able to get the 'feel' or writing it and you get used to it. Of course, if you want any help with that, you can always check out the Beta Corner or the stickied thread about helpful links. I'd also suggest reading to get a bit of foundation.
