For 1:
I did use groups for structuring my works, one for foreground, background, sky, clouds, even every mountain got its own, also for foliage there were sometimes several groups, to split everything in groups and layers gave me more freedom for afterward correction of the different parts, moving things around. It was not seldom that a background mountain was moved more into foreground or the other way around.
I don’t know if this will help you, it may or may not suit you, so don’t try to slip into other people’s suits with pressure, a suit that pinches doesn’t fit!
For 2:
Here, you learn how to make brushes do what you want them to do!
For 3: Plugins:
Pigment.O plugin
A must-have for power users is Shortcut Composer v1.5.4 - Plugin for Pie menus, Multiple key assignment, Mouse trackers and more!
Paint selection (test) Can make special selection needs much easier. But its original download link is broken, you need to go to this posting where you find a new location for downloading it.
And this is a really powerful one reaching out to get a real bummer, currently it combines at least 3 plugins: [In Development] Tablet Friendly Accessibility Plugin (now “Touchify”), which replaces the combination of KanvasBuddy - a Minimalist Toolbar and UI Redesign V0.2 respective its successor Krita UI Redesign v0.5 alpha plus the initial version of “Tablet Friendly Accessibility Plugin” itself.
Docker Under Cursor - make docker display in mouse position
BuliCommander, a very versatile orthodox file manager in Krita!
Plugin - Reference Tabs Docker
For working with many pictures: Open Documents Docker (ODD)
Maybe these too:
Actuator - Automate Sequences of Actions : Krita Plugin [paid]?
Michelist