I have an x56 HOTAS, and what everyone is telling you is correct. But one thing that the game doesn't do is tell you what is what when it comes to the Joystick numbers.
Say on the main joystick, when you look at the Logitech program that comes with the joystick for setup/changing stuff, they give you one set of numbering identification system (A, B, C, D, Pinky, etc.). And while this helps kind of....well not so much in the game config system.
In the game, when you are trying to program the settings to a switch, it gives you a different set of numbers (JOY1, JOY2, JOY3...JOY24, JOY25, etc).
If you are not use to this (I know I sure wasn't) it can be a bit confusing. So, as Hooplah posted above, print out the sheets so that as you add an action in the game, you can take note of where it is on the HOTAS, AND VERY IMPORTANT, what the game calls that position. That way, if you have to go back in and make changes to something, you know which button it is, and what the game recognizes it as...I also took the printed copy that I marked with my layout, and taped it above my monitor. That way I had a ready reference sheet to look at in times that I was busy and couldn't remember exactly where my Lights or cargo scoop were located.
Also, in the event that you have to do an entire reload (doesn't happen often, but it can happen), you have a list of what and where everything is suppose to go to. Making it a heck of a lot easier to deal with in that event.
Just a tip...hope it helps Commander, see you out in the black!
Michael Charlie Golf signing out...