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Alright everyone, let me start this with:
1).+------------------------------------------------------------------ Preface.------------------------------------------------------------------ +
A) I have very little idea what I'm doing 
B) I'm not the best at explaining things ( even more so over text )
C) If you have problems I will do my best to help you, but I most likely won't be of much use 
D) There is most likely better/more efficient/easier ways to do all of this, this is just how I have learned to do it :/
And finally
E) I am in no way an expert, pro, or very knowledgeable at all about Popcorn, but I am willing to share what little know how I have with y'all ;D
Ok! with that out of the way lets get into this!
I'm going to start assuming you know the basics, if not go check out the guide Celeress wrote here.
After that we can start 
2).+------------------------------------------------------------------ Setup.------------------------------------------------------------------ +
I have set up a bare-bones base for people to use if they want:
Download.
The wings we will be editing will be the base wings above, so export the folder in the zip to your project folder.
it should all look somewhat like this when your done:
I use my "Yeron's VFX" folder to keep all of my projects in one place. I would heavily recommend doing this! Your folder should look like the above screen. *Pretend "Demo wings" is "Base wings"*
Alight now you have all of this we can launch PopcornFX!
So launch it and open your project, hopefully it looks like this:
{Edit: my previews never work, your might or might not I dunno :/ }
Now double click the mastery left wing, should look like this:
Now that's a lot of orange ;P
But don't worry we will fix it {enter point of there has to be a better way to do this}
Open the first menu (wing_0)
Now look for CParticleRenderer_Billboard, should be under Renderers.
Click it, and look for Diffuse and AtlasDefinition.
[If your window didn't look like the picture click the path text for Diffuse, and navigate to your texture, vfx_wings_simple_mastery_01 in this case]
Click the box for Atlas and find AtlasDefinitions folder in your project folder, then select the 8x1 you copied in there.
Now go through and repeat the above for everything else in the sidebar 
It should help somewhat by telling you what file it's looking for.
After you have gone through and fixed everything { also known as orange-begone }
It should look a little something like this:
IMPORTANT: ALWAYS ALWAYS ALWAYS BE SAVING, YOU CAN HIT CTR+S TO SAVE QUICKLY.
Great, now follow the above for character_wings_simple_mastery_right_01, aren't wings fun ;D
After that you should have a good base for making your wings, I would copy the folder and make a backup.
From here on it's mostly trial and error, half the fun is the exploration no? ;P
3).+------------------------------------------------------------------ Basic wings:------------------------------------------------------------------ +
Alright now it's the meat and bones!
Open the texture folder and find the wing texture, make a copy, now rename it to something (in this case I'll name it demo_wing.)
Now open the file, it will be .dds format, I personally use Mangastudio for all of my art, unfortunately it doesn't read .dds.
So I export it as .png and open it in aforementioned program.
From here I draw the texture, in this case it will be... hum... how about a rock wing {counter intuitive I know}
Here's what I ended up with:
I make the background to help with visibility ( mostly on white wings, mostly personal preference ) and add a red line down the middle to give me an idea of how the Atlas will split it.
Now you have your texture go back to Popcorn.
Now either delete or disable all of the wings EXCEPT wing_0 (same with wing_grow, delete all but 0)
Everything should look a little weird, for some reason moving things around and deleting make the effect spawn again, just hit the little nuke icon up in the corner or CTR+R
You should have Wing_0, Burst_small_4, Wing_grow_0 Sparkles_1.
Alright!
open wing_0 and change the diffuse to the texture you made. It should look really odd, bu that's ok! We will fix that right now go to your Trove AtlasDefintions folder, where you got the 8x1, and find 2x1. Now copy that to your folder.
In Popcorn click the Atlas under Diffuse, now select the 2x1 definition.
Still look weird? Probably, change the color down below where it says CParticleEvolver_Field and color.
Then what you can do is go back to the CParticleRenderer_Billboard and scroll down until you find "AxisScale" and change it around, I set mine at 3.
[Edit almost forgot, do the same with wing_grow_0]
Now do the same on the right wing.
Now you should roughly have a wing set!
Now what you need is a folder called particles -> in that folder another called FVX -> in that one you put your Particles, Textures, and AtlasDefinitions folders from your project.
Now zip up your first particles folder and name it.
Finally load that up in modloader and boot the game up!
You're the proud new owner of custom wings! 
Ninja edit: If they look really white like here, mess around with the y curve in the color field, or the colorcoef field, add it in the fields node like this:
{Edit: Thanks Thelgmo for clearing up these icons:
Originally Posted by TheIgmo 
}
then click the +
After that add a new field under state_0 and select ColorCoeff.
Fiddle around with that and see what happens!