First : should i connect the cable witch came from the 2 rotatory joystick the way i have done on the pic incuded (with the red tainted part of the connector up side) and is there a threat of destroying the board and potentially the IPAC if i power the Control panel with theses badly connected ?
Sorry, not sure can maybe help more if you post a picture of your joystick PCB. I can tell you now that, if you don't own a multimeter, you can still sometimes visually identify the electrical ground trace or plane of PCB by looking up the datasheet on any IC's mounted on the PCB. The ground of the IC should be connect to the ground plane or trace of the PCB. You could use the same method (just get a meter though, really) to identify the +5V. If you can find the +5V and ground on each circuit board then you just have to match them up. Then you're components will probably be safe.
Second : the CW and CCW connectors...
How come there are actually two of them for each? Should i use the left of the right one ? Maybe there is a ground in each CW/CCW ? If so is it the left or the right one ?
Same question : i don't want to destroy the IPAC and Rotary interface if i miss the wiring
I suspect that since "To Keyboard" is printed next to the CW and CCW pairs that it is designed for a a keyboard hack or encoder. That means that they probably trace directly to the normally open contacts of the 4066 quad bilateral switch. As such, that probably means that when you turn the rotary, the PICs pulse the contacts open and closed. This is to emulate rapid keypresses when you wire it up to your keyboard encoder....I think. I think for your IPAC you wire one contact of each of the CW and CCW sets to a common ground and the other contact of the set gets which ever input you choose. The polarity should not matter as the interface is (essentially) just opening and closing the circuit, same as when we push buttons.