Edit1: Not happy witht he response to Eluvan, so I'll try again. The question is very good.
Yes, I do take cover into account. And yes, it is totally behind the scenes. Sometimes when a normally assured shot from a ranged character flies into the wall instead it is because of cover. But I do assume a few things:
1. With properly posted maps, the players should be able to figure out if cover is in their favor or not.
2. Cover typically only buys the character a +4 to AC. While this is significant, these have been warm-up battles for the PCs ...
So, I guess in the long run, Yavaran striking with the opponents behind cover is not really surprising. He is quite an excellent shot - and precise shot does help some. But, Yavarin has also had a few nice rolls, too. But yes, cover is taken into account. If you have any questions during the game about a cover situation, just ask away. Or, if you want to make sure I am taking into account a cover situation that affects your PC ... just put it in an Sblock as Engrishonly did for his last attack with Eva. Any of that type of stuff you want to put in there is appreciated.
Edit 2: Still not entirely happy.
A couple other things to consider. Geeo (no offense intended, JonnyFive) technically falls under the "low obstacle" category size the guy is a small character and the gnoll is, well, not. Since Yavarin is closer to Geeo than the Gnoll, he receives no cover from Geeo. As to the rest of your characters - yes, you do provide cover for one another as described in the PHB.
In general, I do try and stick to the "cover provides a +4 to AC" rule. Soft Cover (cover from other living, moving, gyrating (?) creatures) never gets ruled as being eligible for Total Cover since the soft cover "combatants" are technically always in flux of movement. To receive Total Cover, one must be behind a solid wall, a significant tree, or some other large (probably) immovable object that is larger than your character's body.
Now, I think this gives an answer to Cassient's spell dilemma. A good rule of thumb is to "hypothesize" a probable AC for the enemy and add 4 to it is they have cover. Then, evaluate the character's ability to strike. If reasonable, go for it.
Oh - one more thing. The comment I made earlier about the spell being a miss either way had nothing to do with cover ... it had everything to do with the fact that the die came up as a 2. Even without considering cover Cassient would not have succeeded on a ranged touch attack.
But as I said before, this is a good question. Hence, why it has taken me 2 edits to get comfortable with my answer.