So there’s a color for each qube and this color is applied to icons of the applications on this qube. How does this happen exactly, are there an icon for each color? Overlay? And most importantly, how can I change icons for an individual qube’s app? So for example I have firefox installed in my template and two qubes: personal and work. So if I want to use two different icons(not just the color) for personal and work, how would I do that?
How does it work?
The actual qube icons for a template, AppVM or a DispVM are actually different icons for each color, and they have been rendered in all sorts of different sizes. (And some sizes of the gray ones were actually black…so gray qubes were black in my Qube Manager because they just happen to be one of those sizes. I eventually just made my own versions of those. Unfortunately I don’t remember which sizes. I don’t know if they ever got fixed in the distribution.) These mostly appear in /usr/share/icons/hicolor/22x22/devices (change 22x22 to other sizes). Those are .png files. One of the subdirectories of hicolor is “scalable” (/usr/share/icons/hicolor/scalable/apps) and those icons are svg files. There is also a set of icons in /usr/share/qubes/icons. [Beware: unless they’ve fixed something, the dispvm icons in that directory are the old “padlock” style so those will show up instead of the standard dispvm icons in certain places and you will likely tear your hair out trying to figure out why. I finally just made sure to put copies of the correct icons somewhere and just make sure after updates to copy the correct ones.]
These directories appear on both dom0 and domUs (i.e., other VMs).
That’s for qube icons.
I know for other icons like firefox, they actually do apply a color overlay in real time. (And I wish there were a larger firefox icon out there by default; by the time you make a desktop shortcut out of the one that’s there, it’s just a blob.)
That doesn’t help you change icons, I know but hopefully it gets you started.
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Oh, yes. For me the icons are in other sub-directories of the /hicolor/ folder, I don’t know based on what logic these icons are sorted though. And for the overloay, I just can’t find anywhere where I can modify this… these colors are very annoying for my eyes 
you can do it but just for shortcuts not for apps on menu