Well, one way is to have the MLP characters' species - specific traits play a role. Pegasi could use their flying abilities for reconnaissance in the Newport area. Earth ponies could be great at handling the physical tasks on the base. And in terms of the story, the cutie marks of the ponies could be related to their roles in the Navy OCS. For instance, a pony with a cutie mark related to maps could be in charge of cartography in the military unit. The values of harmony and cooperation from MLP FIM can also be shown in how the characters work together in the Navy setting.
Incorporating MLP FIM elements into a Navy OCS Newport fanfic can be done in multiple ways. Firstly, the appearance of the MLP characters can be a contrast to the traditional military environment. Their colorful manes and tails can make them stand out. Their magical abilities, as mentioned before, can be used in various military tasks. The social structure of the MLP world, like the different pony tribes, could be translated into different units or groups within the Navy OCS. For example, the unicorns could form a special unit that deals with more technical or magical - related tasks, while the earth ponies are in charge of more hands - on, physical labor. The friendship and loyalty that are so important in MLP FIM can be the driving force behind the characters' actions and relationships within the Navy OCS Newport setting. This would create a unique blend of the two very different worlds.
The MLP FIM elements can be incorporated by having the characters use their magical abilities in a military context. For example, a unicorn could use its magic to help with navigation or communication during naval operations. Also, the concept of friendship from MLP FIM can be a central theme, like how the characters support each other through the tough training in Navy OCS Newport.