PKMN has 3 main phases that the game cycles through over the course of play: Free Play, Episodes, and Downtime. A session will usually involve a mix of at least 2 of these phases.
Free Play is primarily about exploration and social interaction, and leads into Episodes through hooks and opportunities players choose to follow. Preparing Free Play segments usually involves having environments and locations ready to be explored, local Pokemon and NPCs to meet, and problems, mysteries, and encounters that can lead into Episodes.
Throughout Free Play, players will encounter things they may want to explore further
Episodes are a set of connected scenes and encounters, around a similar theme or with a shared goal. Episodes start with a goal chosen by players (though the journey is more important that the destination). This goal could be almost anything, from ... to ... . The GM presents encounters along the way - environments, obstacles, wild Pokemon, other trainers, and oddities out in the world. An Episode is complete when the goal is achieved, or...
(Advice for prepping different types of encounters will be linked here when it's finished)
Downtime is the simplest phase to prep, as it's largely directed by players. Each player chooses 2 downtime actions to perform (eg. bonding with a Pokemon, training, working on a project), and each action is accompanied by a small scene in a location nearby. Players will roll for their chosen action, and then narrate with the GM how the scene goes.
(Once it's finished, there will be a link to the rules for Downtime Actions here)