I ran our first game (Shadows of a black sun) a couple of days ago and one situation that came up was a player wanting to pin down the end boss, Kaa'to.

I had a look through the core rulebook for rules on grappling but it said there are none, intentionally.

I improvised and said that the opponent was immobilised and took a setback die to actions, and should make an opposed Athletics check to break free as a maneuver.

Does anyone have any advice about how to handle this in the future? It seems like a common thing to want to do and I'm surprised there are not more guidelines in the book about it.

From page 211:

Edge of the Empire, being a more narrative game, does not possess specific rules for grappling. Instead, the unarmed combat ruleshave been designed to narratively cover multiple unarmed fighting techniques, including grappling. For this reason a basic Brawl attack allows characters to deal damage to the target's Strain Threshold, and can knock them prone and disorient them. This allows for the narrative of a grapple (which is often intended to incapacitate without killing) without additional rules.

I'd just say follow the sidebar. Use Brawl along with its ability to disorient to narratively create a grapple maneuver.

There are many ways to do it.

1) You could treat it as a normal brawl attack, but let the attack activate the Ensnare quality instead of Knockdown or Disorient.

2) You could treat it as an opposed check, opposed by brawl or athletics.

3) You could make it a competitive check, difficulty being average plus normal defence and talent increases. Winner gains hold and pins or damages opponent.

And there may be many other ways of doing it. Like mentioned above, make it a narrative and use what's there instead of adding to it.

My instinctive reaction would be to have the player make a Brawl roll with the difficulty upgraded. The number of successes would indicate how good a grip the PC got on the NPC; this would be relevant later when he could attempt to break free as an action (needless to say, keeping him pinned would also constitute an action, so that PC can't start doing other things as well). If the player got enough Advantage (at least three, probably four) he could also hold onto the NPC as a maneuver rather than an action. A Triumph would accomplish that and leave the NPC at a severe disadvantage when trying to break free, while a Despair meant the player either fell on his face at the NPC's feet or got grappled himself instead.

The suggestion noted in the book seems like a reasonable alternative. If you wanted to go the opposed check route. I suggest a Brawl check with the difficulty based on their coordination skill or Athletics skill, whichever is higher.

Trigger Knockdown and potentially Disorient. Pretend that it is because you tackle them down and are pinning them (though you don't take the Prone penalties for it.) They can maneuver to "stand up" (aka get on top of you). Another maneuver could disengage them, as they roll off and away from you. Perhaps you could allow them to spend a Triumph to Ensnare someone that they have successfully Knocked Down with their brawl? And a second Triumph while they are ensnared in this way could attempt to choke out the opponent?