The reason we have so many controls is that different aircraft have different ways of doing things: what works in a Hurricane might not exist in a 109 and vice versa.
The way to get to grips with it all is to spend some time in the stock free flight missions with each aircraft (preferably starting on the ground) and look around the cockpit.
Use the mouse to hover over the controls and see what each one is and what exists in your aircraft, so that you have a mental list of things you might want to map to your peripherals.
I use keyboard and stick for the flight critical controls and some secondary ones (like setting the compasses or doing bombsight adjustments) and use the mouse for tertiary controls that are only used once-twice per mission (eg, the fuel selector valves or the floor window on the Stuka, i manipulate these with the mouse).
This makes it easy to have a few keybindings that i can remember, while using the mouse only for non-critical controls so that i won't need to be clicking things during combat.
In short, think in terms of individual aircraft cockpits and not in the old way of "pressing button X will do this in every aircraft" and you'll do fine
