The basics of an event like this really aren't as difficult to set up as you might think, but there ARE some important considerations that go into it. Start by looking at the example maps in essentials. On Route 3, the one with all the example trainers, is a rival encounter. That has the basic structure of what you want, an event which triggers a character moving on screen. There are, of course, some things you'll need to change:
The graphic (naturally) to the OW of whatever pokemon you want to use.
You'll remove all the dialogue and trainer battle stuff so that all it does is move across screen.
Determine whether you want the player to be able to move while this event is running - this will affect how far you have to extend the pokémon's movement so that the player doesn't see the end of the animation.
Determine what triggers the flight, whether it is the player stepping on a certain tile (player touch) or when they enter a certain map (autorun).
Make sue to set a self-switch for the event.
So that's what you need to do to get a bird to fly across the screen. You can definitely make some of these areas more involved, but those are the basics.