PKMN has 3 main phases that the game cycles through over the course of play: Free Play, Episodes, and Downtime. These phases each support different tones and paces of play, with Episodes providing structure for focused adventure or scenarios that are easy to prep, Downtime to allow players to direct scenes recovering and pursuing their own projects, and Free Play for freeform exploration and roleplay.
A session will usually involve a mix of at least 2 of these phases, but this isn't a necessity, and Episodes in particular may take a whole session or more.
These rules are designed to facilitate easy flow between different paces of play, and give a structure to support a good balance of different types of scene. They don't need to be followed rigidly, and your group's preference will influence how much time is spent in each phase.
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...
Episodes are supposed to provide a structure and thematic throughline for action, and are useful for prepping one-shots and individual sessions.
(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)