Hello, Kerbalnauts!
I require some Assistance and / or Input of Experience with the Following:

Issue 1) Engine Glow - Test 1 2 3, is this on...?
I've noticed my Engines won't glow / visually turn on when throttling up, they just stay black instead of turning red inside. I don't mean Reentry Heat, I mean the Engines themselves won't glow. Am I missing something here...? Is it some Setting? I never had an Engine showing the overheating Bar either yet, is there a Setting somewhere which I accidentally turned off? Please don't say it's gotta be my Video Drivers, that would really suck...

Issue 2) Subassemblies - Do you even sub, Bro
How to Subassembly?! I've seen so many Videos using these, but I can't find it anywhere in the GUI. I accidentally, once, somehow, had that Subassembly Field show up in the bottom left Corner so I know it's either there or I'm going crazy, but I have absolutely no Clue whatsoever how I made it appear.

Issue 3) Force-Click Punch-through
Also, other Stuff I noticed is, in the SPH and VAB, whenever interacting with the GUI, it'll click THROUGH the GUI very often as well, detaching Parts from the Ship if GUI and Ship overlap.

Issue 4) Selected Tool - It's a Lie
Another Thing is, the selected Tool. One might be displayed as being active, but as soon as I try to use it, turns out Place is the one that's actually active despite not showing as such. Mostly happens when moving Parts along their Axis, and then deciding to delete the selected Part with DEL. Which is 1) extremely handy and prevents misclicking and unintentionally detaching other Parts, and 2) what I'm extremely used to from the Besiege Editor, I believe.
That made the whole Deal of Controls in the VAB very hard to wrap my Head around at first as well.
Besiege has such a good Editor. It really bugs me ALOT not being able to center Cam on Parts.

Issue 5) For the last Time: NO, I didn't want to pick THAT
As mentioned above, it happens extremely often that Stuff I didn't click and wasn't highlited a Second ago is being picked instead of the Stuff I intended to pick, which leads to me switching over to a different Tool that doesn't immediately detach Things and therefore requires me to wait through long CTRL-Zs over and over - and then ends up in me forgetting that the "selected Tool Bug" will make me have to CTRL-Z the next Time I click anyways if I don't explicitly change Tools again.

Issue 6) Derp
I forgot what it was, but it was kinda important. I'll add it back in later as soon as I remember.
Probably right after posting this.

Hello! I'll try to answer to some of your questions (though I tend to mess things up in the VAB myself ^^)

1 - Engine glow : I don't really remember the engines "glowing" when I throttle up, apart from a few specific ones like the ion engine. I'll have to check. Or maybe you were talking about the flare they're throwing when they're active (in which case I do have them, and you may have a problem in your graphical settings?)

2 - Subassemblies can be accessed by clicking the big arrow above the parts list. that will get you to the "advanced" part selection (subassemblies, filtering by functions, etc...). Then simply drag your assemblies into the box and name them. I love to use it for my science or electronics service bays.

3, 4, 5 : Dunno, I tend to be a clumsy oaf in the VAB. I should probably look at that, too. (And consider yourself lucky : For the longest time, I didn't know about ctrl-z... ^^)

6 : ?

Issue 1) Engine Glow
Rockets do have a Trail of Fire and Smoke, Jet Engines have just Smoke. No Sparks, no Flames, if that's what you meant... but I for sure have seen Jet Engines glowing red when throttling up, and they don't do that over here. They look like cold Metal blowing out some Smoke. How do I fix that, where's the Setting for that? For a long Time I assumed that was added by some Beautification Mods until one Youtuber stated he had to remove all Mods due to the Update, and the Engines still were glowing. Also, Ion Engines won't glow blue either, they just stay the way they are, black. THIS SUCKS.

Issue 2) Subassemblies
OMG I didn't even know that was a BUTTON in the first Place. I always wanted to be able to sort and filter like this, too...! Geez, no Tutorial ever mentioned it, nor did I ever see Youtubers click there either. Thanks a lot.

Issue 6) ...
Still didn't come back to me, but I'm playing right now. So, Chances are I will soon encounter and remember. Yeah... Scumbag Brain. It likes to do that.

Overheating bar and overheating glow can be turned on/off with F10/F11. Maybe you pressed one of them by accident?
Note that engines overheating at launch doesn't happen very often. You will see it mostly when you crop togeteher several powerful boosters. I see it far more frequently during reentrry after an orbital flight (suborbital generally isn't speedy enough to have a real rentry burn), or on exposed non-aerodynamic parts (like decouplers, wheels and solar panels) when I go hypersonic too soon during my ascent.. No problem, sharing tricks with other players is half the fun of this game :)

Ah well, there are little Bars that DO show up all over my Craft, but not next to the Fuel of the Engines in Staging. Never saw that. Other than in Youtube Vids. Also, it's very NOT USEFUL having like 20 different little Bars popping up all over my Ship and not being able to tell them apart or see how bad some of them are because they're all overlapping each other. Those should have been in a List at the Edge of the Screen or something, and Mouse over / Click the Bar should highlight the Part it belongs to. Just like right clicking the Staging Icons opens the Right Click Menu for the according Engine. Oh wait, it doesn't. IT DEFINITELY SHOULD. Things are just way do fiddly and impractical like they are right now, there's so much Room for Improvement. Any Mods out there doing that Stuff...?

Anyways, I'll try punching F10/11 next Time to see what it does for me. Not being able to open the Controls from Inflight [sigh] - or (re-)assigning Action Groups in Midflight or after Docking - is quite annoying. Since I didn't know the specific Control, I once just pressed every single Key on the Keyboard, so that might have messed something up with the Engine Settings or something, I just need to know what it could have been. Do Things like that persist through multiple Flight Sessions...?

Though - I believe Jet Engines just won't glow for me. I've messed with all Settings on Max, even Fallback Shaders, whatever those are, and put an Engine on a Stand, firing that up and waiting for like, 5 Minutes. Not a single hint of redness anywhere in the Engine, just blowing Smoke. See the attached Image, top left Panel. That's what my Engines look like all the Time at full Throttle.

When Reentry happens however, or generally Velocities over 1.000 m/s, like in the second Panel, the Heat makes it look almost like it's supposed to, glowing red inside - see the third Panel, where the Engines are in Fact switched off. So, why does that "Heat Glow" work, but not the normal "Engine Glow" like in the forth Panel from Youtube?!
I dun geddit. I wanna.

Thanks though.

Don't think that's it. Ion Engines still don't go blue. When did said Change happen...?
*Edit: Alright, found the Threat about Engine Glow.

Now I just need to find said Mods.
Game's plain broken without.