For the theme you can choose from already existing Themes from Menu Bar, Settings > Themes. Or you could make your own either from scratch or based off existing ones. To create new ones you’ll want to create (if not already available) a folder named color-schemes in your krita resources folder. In the folder make a file with a name of your choosing with an extension .colors and change values to your liking.
Content of the Theme file (without the explanation “# text” stuff, you want to remove that):
[ColorEffects:Inactive]
ChangeSelectionColor=false # Not sure if used
[Colors:Button]
BackgroundNormal=45,45,45 # Buttons background color
ForegroundNormal=235,235,235 # Buttons text color
[Colors:Selection]
BackgroundNormal=83,114,142 # Color overlay for sliders, currently selected layer, etc
ForegroundNormal=255,255,255 # Text color for above mentioned stuff (like brush opacity %, size, layer names, etc)
[Colors:View]
BackgroundAlternate=36,35,35 # Alternate background color for certain GUI elements (like checkboxes, alternating lines in shortcuts window, etc)
BackgroundNormal=28,28,28 # Main Background color for most GUI elements
ForegroundLink=216,216,216 # Color of link text (such as welcome screen News links)
ForegroundNormal=235,235,235 # Text color of everything not mentioned above
[Colors:Window]
BackgroundNormal=50,50,50 # Borders/titlebars color of windows (such as dockers or toolbar, toolbox, etc)
ForegroundNormal=235,235,235 # Text color of said elements
[General]
Name=Color Scheme # Theme name (as seen in Krita Theme list)
Alternatively you could try using a plugin to create new schemes:
Plugin: Theme Creator Extension - Resources / Plugins - Krita Artists (krita-artists.org)
As for the preset icons, there are multiple ways of editing them yourself. In Brush editor (preset settings) when saving new or overwriting changes to existing preset you get to edit its icon, you simply draw there, add icons from library, load an image or load scratchpad content (from Brush editor). Another way is to go to your resources folder > paintoppresets folder, find a brush preset you want to change icon for, open it with Krita and change the icon to your liking and save the file.
Have fun customizing Krita to your liking! 