Secrets of the Grave allows you to affect undead with mind-affecting spells as if they were living, even if they are mindless. Interpreting how that works in any given situation is a case of breaking it down and a little cross-referencing. So, essentially, the class feature does three things:
1. Allows you to affect undead with mind-affecting spells
2. Allows you to affect undead with those spells as if they were living targets
3. Allows you to affect undead with those spells even if they are mindless
A little cross-reference to the undead traits in the Bestiary shows us undead's immunity to mind-affecting effects includes: charms, compulsions, morale effects, patterns, and phantasms. But (and here, I think, is the bit you're probably after) other immunities granted by having undead traits are listed seperately, such as: death effects, disease, paralysis, poison, sleep effects, stunning, non-lethal damage, exhaustion, fatigue, etc., etc. These other immunities are nothing to do with being affected by mind-affecting spells or not.
So, to your examples:
Colour Spray normally has the potential results of unconsciousness (living things only), blindness, and / or stunning. So when out Dirge Bard casts that spell on a zombie via Secrets of the grave, we need to run down our check-list of what effects get through. The mind-affecting aspect is okay, despite the zombie being both undead and mindless, so we move on to the specific effects. Blindness immunity isn't listed anywhere under undead traits, so that effect is fine. Immunity to stunning is listed, and seperate from anything to do with being mind-affecting, so that effect of the spell does nothing. Unconsciousness immunity isn't listed (technically unconsciousness is neither a sleep effect, nor an exhaustion / fatigue or non-lethal damage effect) and the Dirge Bard gets to affect the zombie as if it were living, so the 'living targets only' clause on the spell's unconsciousness effect also doesn't apply. So the zombie can be blinded and/or KOd by the spell, but not stunned.
With the Lich in the corner, and no space for Shinami, he decided to poke around the area in which they saw the Lich for any clues on what they were dealing with.
Perception check to search the torture area? 1d20 + 11 ⇒ (11) + 11 = 22
"Are we it? What were you expecting, might I ask?" Thanatos asked as he mentally commanded Nyx to fall in step behind him and to pull his hood further down across the smiling skeleton's face.
"Defiler of forests? I'm sorry ma'am, but I think you have the wrong people. Who are you looking for?" Thanatos asked as he squinted down the road to see who was talking to the party.
Shinami, seeing that half his friends have fled the cavern sees Brom across the island attempting to fill the Chalice.
Crap.... I can't reach him. The lich is between us. There's no way I can stop Brom... I'll just have to focus my efforts on the lich. I don't know much about lich spells, but maybe if I can keep him from talking, he can't cast spells...
Shinami dashes toward the lich and attempts to silence him, a forearm across his mouth, someway to keep him silent.
crunch:
Grapple 1d20 + 11 ⇒ (3) + 11 = 14
If successful, maintain Grapple also plus sneak attack for maintaining. If not successful, then normal grapple, no sneak attack 1d20 + 11 ⇒ (19) + 11 = 302d6 ⇒ (6, 2) = 8
Shinami whispers "Cecil, I hope you can hear this, but Brom looks like he just got mind controlled and there's an island down here in a black lake and there's a lone creature on it. I think it's the lich. Come up with a plan quick please!"
"Alright, so Brom and I will scout ahead and we'll whisper what we find to Cecil? This sound like a plan? Hopefully you can use the information we relay back to you to come up with a strategy."
I'll do it 5 times unless something interupts us in the time it would take to do it. I wasn't going to use so many charges, but then I didn't expect to roll so poorly. Stupid 1s...
Shinami will check the double doors for traps and the area around it.
Once through double doors, continue to check for traps while exploring. Once enemy is found return to main force or have Owen report telepathically while Brom and Shinmai hides.
"Should I take Brom and go scout ahead? Let's not have Ms. I Knock Everything Over When Sneaking (or Ms. Knockers for short) wake up another room of guards, aye?" Shinami winked at the armored ladies.
"Well then. We should proceed carefully and treat every guard with gentleness after this scene. Nonlethal wounds from now on, aye?"
Shinami whispered, disgusted with the scene.
They're soldiers deep in the citadel, right next to the supposed Queen's chambers, the chamber of DOOM. We pop in, they pull weapons. First fight that starts, no indication that they are anything but the Queen's loyal guards. Wasn't till after a few were fillet that there was any sort of hesitation in their eyes, but most would just see it as "Holy hell, these guys are good, do we fight them, run, or get reamed by the queen?" So they stayed and fight. And died. Wasn't till that last bit where the one guy gets flung toward Armen's sword that there was blunt indication that they had no control over their actions.
Shinami rolls to the next one and (if it's a man) beats him down senseless (if it's a female) "Hey pretty lady, mind helping us out here? Better than getting killed by my friends here, yes?"
If a pretty lady then diplomacy check 1d20 + 12 ⇒ (19) + 12 = 31. If that fails 2 grapples due to maneuver master and haste 1d20 + 12 ⇒ (4) + 12 = 16, 1d20 + 12 ⇒ (16) + 12 = 28
Owen adjusts his grip and shatters the ankle, bringing the guard down screaming in fear.
Couple things Shinami. 1, your damage is 1d6 normally. 2 your to hit should be +10. 3, I'm not doing a map for this fight. That said, your internet is terribad so I will adjust your action for you.
Shinami dives into the room: litterally, and rolls behind a guard. he punches him hard twice.
36 damage.
1d6 for fist damage, 1d6 for fire damage from fire enchantment on the brass knuckles remember? Silly DSP. And I did forget the +10 bit. Thanks for that.
Maps not set up so I can't tell if I can flank someone or not for sneak attack. If I can, DSP just move me there since you know how atrocious the internet is here in the middle of nowhere and include the sneak attack dmg. Thanks bro.
