Right now the code doesn't handle more than one joystick but that's being fixed. Also, although it supports 6 axes it only polls 4 which means that it will only gather info on X, Y, rudder and throttle (if all on the same joystick). The new joystick code will handle the same number of buttons (32), go from supporting a 4-way coolie-hat to an 8-way, properly handle all 6 axes and do all of this for 2 joysticks.
This new code probably won't hit an official version of FS2_Open until the next full point release but should be in test builds late next month. The new joystick code requires the new control config code which in turn requires the new pilot file code. There's a lot that has to go into this which is why it's taking so long to hit the public.