FS2_Open control scheme currently only allows you to bind five analog axes:
Pitch
Roll
Yaw
Absolute throttle
Relative throttle
...and the rest of the controls are all digital; only keypresses can be bound to them. Control, Alt and Shift keys are at your disposal to increase amount of key combinations, though.
Personally, when playing something that allows glide and lateral/vertical thrusters (Beyond the Red Line, some ships in The Babylon Project), I usually bind W as afterburner, S as rear thruster, A as left lateral thruster and D as right lateral thruster. If I don't have joystick or I choose to use mouse for greater accuracy, I might have Q and E bound to roll.
And yes, I sacrifice up and down thrust for better forward/backward control. If I had a HOTAS throttle, I would definitely bind up, down, left and right to a hat switch on the throttle, along with buttons for afterburner and rear thrust at other finger tips.
On FS2, I have a similar set-up except A and D control roll when I'm not using joystick.
