I recently got the x52 pro and its true,theres so many bottons you wont know what to do with them/yet configure them
and thats the problem
all the botton on my joystick cant be configured
like on the throttle quadrant i would like to use the rolling things attatched around Fire E and and that little I BOTTON but i cant
and i would like to use the mouse axis on the joystick but cant and the scroll wheel on the front of throttle i cant use that
and the pinkie switch on the joystick it self

so if anyone can tell me how i can fully configure these it would help lots!
other then these few problems i have nothing but good things to say about this joystick
its precision,its craftmanship,everything,has really help me become a better pilot

i got the X52 Pro as well, here's how i've configured it

XY axes - ailerons and elevators (just like everyone else  )

twist stick axis - view left/right (axis) --i have the pedals as well, so i rarely use the twist grip

throttle axis - throttle

big rotary - elevator trim (makes a world of difference having your trim mapped to an axis)

small rotary - mixture

slider - spoilers

now the buttons, i've mapped them with different functions to each mode, not all buttons are changed, so i'll just post the differences after mode 1:

MODE 1:

trigger/first stage - null
trigger/second stage - parking brakes
2/fire - release dropable objects
3 - change view category (A key)
4 - change view (S key)
5/C - sound on/off ( i had to map this to a button because of an annoying sound problem i'm having)
pinky - ATC window
right toggle - gear up/down
middle toggle - flaps
left toggle - null (i haven't set everything yet... just too many buttons  )
primary HAT - pan view
secondary HAT - move eyepoint

D/throttle thumb button - full throttle (F4)
E - gears again ( don't ask why)
mouse wheel - +/- (controls zoom)
mouse wheel click - backspace (defaults back to zoom)
throttle HAT - pan view (redundant-- useful for flipping switches around the cockpit)

MODE 2

3 - flaps up
4 - flaps down

throttle HAT left/right - change view category
throttle HAR up/down - change view

MODE 3

secondary HAT (left, up, right, down) - 1, 2, 3, 4 keys respectively (very useful for handling ATC)

as you can see, i'm not done mapping this thing either, and i've had for some six months now... but there's no rush... you should create a basic generic layout first, then add more commands as you feel the need for them, this way, you''l get your most used controls right where you want them, and you won't have a very complicated layout to memorize right from the start

now, the trouble you're having with not being able to map the controls, i believe are caused by using the stick on 'no profile' mode... this mode causes many features to remain deactivated, such as the  mini-mouse...
also, most games can't see all the buttons on this joystick, so it's pretty much necessary to use a profile, even if it's a basic one...  but you'll see in time that using the SST software is much better than mapping commands on the in-game screens, it provides a standardized command mapping interface with several neat options, such as banding axes and macros

hope this helps

Cheers