you need to think a little about what functions you will need in combination with others.
eg for me i need to be able to use main weapons, secondary weapons and all 6 axis of movement (pitch, roll, yaw, main throttle, 4 lateral thrusters) at the same time.
given that i opted not to use the hat switch for lateral thrusters as that then blocked my ability to use lateral thrusters and secondary weapons. instead i used the throttle rocker switch (left+right) and buttons 5&6 (up+down) for my thrusters. i use the hat for power management which is also crucial in combat. i will admit while this has worked well i still want a better solution so i've just put in some ebay orders to follow this guide :
http://www.instructables.com/id/Add-a-little-two-analog-axis-thumb-joystick-to-you/?ALLSTEPS total cost was about £10, though i added an extra 3-way navigation switch in which i'm hoping to frankenstein onto the joystick for extra buttons there (so that cost an extra £2 on top). i plan to put that where the rocker switch is so my 2 little fingers could be using that. i feel that is a better solution than anything the x52's and the like have to offer. none of them are built for a spaceship, so none of them cater for 6 axis of movement, expect exciting new toys to arrive on the shelves after elite single handedly caused stock issues for all popular joysticks. the manufacturers will probably realise there is a gap in the market and another big space game is due to hit next year. there are already 3d-printed 3-way thruster throttles being built by the hacking/making community.
anyway, back to the stock stick. because elite has some wonderful built in support for making your own shift buttons i used that to get 3 different types of shift: combat, navigation and UI. combat is things like cycling targets, subsystems and weapon groups. navigation is things like landing gear, FSD and supercruise only (for when a pesky planet is in the way of the system you want). UI is left and right UI panels in combination with the hat to select which one. it might seem like overkill on the shifts, but if you think about the type of action you want to do, then you're just pressing the button associated with that type of action and then one of the main buttons to do that action.
so i use the hat switch for power management. if i press the weapon shift it then cycles hostile targets on left/right and subsystems on up/down.
to get into FSD i press the nav button together with my boost button.
for the left or right UI i press my UI button together with hat left/right.
so in that regard lots of shift buttons can be quite intuitive.
i don't think it would help to give you much more info than that as placing controls in an intuitive place to you is important, and we all think differently. hopefully my pointers will help you organise things in a way that doesn't handicap you due to conflicts over what your fingers can do at any given time
