-Charm! Sooo, book says that when you get a threat on Charm checks, then it can lower your standing with the person you're convincing. So maybe the person you're charming just begrudgingly does what you're asking, but it kind of ticks him off that you'd ask, for instance. Additionally, if you were trying to charm 3 people, maybe a success and 2 threats means that you only charmed one of them. Maybe it's their boss, so the charm goes through, but maybe the henchmen are a bit ticked about it. Maybe something comes from that, later on? Of course, this is situational, and it doesn't work in all cases, but that should give you an idea.
-When they fail a roll but get advantages, I try to think of a way that they could "fail upwards." Think of the very specific thing they're trying to get done, and then (almost like a genie trying to twist their words on a wish) give them something else instead. So maybe they're trying to hack into this Imperial officer's computer to figure out a bomb's disarm code, as one example. They fail, but they get advantages. They don't get access to the computer (or at least not the parts of it that they want), but maybe they figure out the officer's itinerary, so that they could go and beat the information out of him. If they're trying to make a coordination check to keep balance as they cross a beam, maybe failure means they fall, but the advantages allow them to catch on the beam before plummeting.
I wouldn't stress too much about the advantages/threats. Also, make sure that you open it up to the players for input and ideas! Especially when it comes to their advantages, and provide suggestions if they seem lost. Don't worry about ignoring some advantages/threats if it's slowing things down. Not every single one needs a dramatic and explosive use. And always refer to healing/suffering strain if you have to.
Question #1: When someone suffers their full Strain threshold, they fall unconscious. Technically your Wookie could have tried to hit them with a melee attack and try to do enough Strain damage to incapacitate them. Maybe they get some Boost or an Upgrade for the target being unaware. If they didn't do enough damage, maybe advantages could be spent on "stunning them in such a way that they don't think to call out for help, or maybe karate chopping them in the throat so that they can't call for help," giving you enough time to make another attack. Of course, is any of that necessary? It's up to your group, of course, but I'd probably just let the Wookie make an attack roll and if they hit/do more damage than the dude's soak, have the guy get knocked out. If he's not some boss villain, and just some thug/grunt, then why not let the Wookie rough him up and keep the suspense and action moving along? Just my two cents :)
Question #2: The AoE of stun grenades is represented by the Blast Quality. By default, all qualities cost 2 Advantages to activate, if they don't specify another amount. If you're just lobbing a grenade at someone, you'll deal damage to them like any other ranged weapon. However, if you have enough advantages to activate the Blast Quality, then you deal damage equal to the Blast Rating (Blast 8, in the Stun Grenade's case) plus any net Hits on the attack roll to all targets (friend or foe) who are engaged to the original target. For example...
Baddie A is engaged to Baddie B and Friendly C. You throw a stun grenade at Baddie A. You roll 2 Hits and no Advantages. Due to a poor throw or other circumstances, the explosion only hurts Baddie A. It deals 10 damage (base 8 + 2 net hits). However, if the roll was 2 Hits and 2 Advantages, then you could activate the Blast Quality. This would mean that Baddie A suffers 10 damage (Base 8 + 2 net hits), Baddie B would suffer 10 damage (Blast 8 + 2 net hits) and Friendly C would suffer 10 damage (Blast 8 + 2 net hits). Then subtract soak as normal.
The Blast quality also has the nice effect that even if the grenade attack is a miss, you can spend 3 advantages to still deal damage to the target and everyone engaged to the target equal to the blast quality of the grenade.
Stun Grenades also have the Disorient quality. If you activate this (paying 2 advantages to do so), then targets suffer 1 setback on all actions for a number of rounds equal to the disorient rating (3 in the case of stun grenades). There are a couple ways you could stun the Gamorean guards. Hit them, activate Blast and fill their thresholds so that they fall unconscious. If they'd still be up after suffering X strain, then you could activate Disorient (if you had enough advantages) and flavor it that way. Though they're still acting, they're dazed.
Also, you don't have to follow explosives rules to the T if it makes more sense to do something else. If those guards were in a confined area, maybe it wouldn't take much to hit them "accurately," and if it was a small space, then maybe don't even bother rolling. Maybe instead it could be a Resilience test to not get knocked out automatically, or maybe don't roll at all and reward the PCs for being prepared with a stun grenade and using it effectively. Obey the Rule of Cool! If everyone thinks it's cool, then go for it!
As far as Stun Damage goes, it operates basically the same as Lethal/Non-Stun/Normal damage. You deal critical hits exactly the same. If the target doesn't have a stun threshold, then they suffer wounds instead, but when they hit their wound threshold they'll likely just fall unconscious instead of dying (though up to you in the end).
Also you can be pleased to know that there is no Game Master's Guide that you need for this. Just having the Core Rulebook "Edge of the Empire" is enough. There are plenty of other supplements with some nifty tools, extra specializations, interesting locales, vehicles, etc. And then there's also Age of Rebellion to play as rebels and Force & Destiny to play as jedi.