I haven't used a joystick since transitioning from Amiga to PC (80468 era!), so I expected to be rusty coming into a HOTAS setup: decades without a joystick and a much more complex HOTAS (went CH Fighterstick + CH Throttle Pro, no pedals) to boot!
Turns out, a decade of (ab)using the Suzo Arcade (best joystick of the era!) payed off in the end after all
! Using joystick to roll and pitch just comes naturally and I can't think of an input device which does it better than a good joystick and main flying accuracy is pretty good.
The multitude of hats and buttons though, that's a bit more difficult to get a grip on. Schemes that other players use are a good way to start. It helps if you're able to decide what you want to do with your left hand and your right hand.
Currently, my flight stick contains all the primary "combat" functions: triggers, target selection, energy management, fire groups, defensive measures, plus headlook. Throttle hand is for managing motion / thrust (forward and vertical thrust, reverse button and boost), Flight assist, Supercruise. Exception is yaw, which is logically not a function of thrust, but I don't have pedals or twist-action. I use yaw more often in flight than lateral thrust, so it replaces lateral where it otherwise should have been. Other miscellanious functions also go on this controller: Landing gear, Cargo scoop, sensor range, UI controls.
I have overrides when landing gear is down where I replace yaw with lateral thrust, with yaw remapped on another hat-button.
I also have an extra button on the stick that acts like a "shift" button to overload some buttons with related functions (FSD vs FSD to SC only; Target vs subsystem Target; etc.)
But this setup is something that I've worked at for a few weeks; muscle memory is not consistent yet. Sometimes, I have to really think what how I want to do something (Chaff! Oh no, that was a Shield cell!). And regularly, I get insight that some things just don't really work as well as I thought they would, or I want to try a different thing (4 way target hat: is left - right target next / prev, plus shift for subsystem, or left is subsystem, right is ship, with shift going previous instead of next). Sometimes, I notice that I often accidentally bump the target selector while using secondary trigger. I'm not quite sure what to do with that yet: secondary trigger is a bit awkward due to the shape of the Fighterstick in relation to the size of my hand.
Anyway, I expect my button configurations to change in the coming weeks as I go on experimenting with a few things. Just keep in mind that in the end, it's the muscle memory that needs to be built up; you need to transition yourself from thinking "I need to press the left button" to thinking "Chaff and Boost!". This takes time to build, but remember that using your controller is also something you've built up over the years. No button configuration is necessarily "natural", just something your hands need to get used to.
