Hi everyone ! Thanks for the all the advice you gave me. I thought about my problem all day long and i decided to keep on my mission.
Since I know that my approach wasn't perfect (I remembered I placed one of the AN/DN at the exact location of Jool's intercept which is WRONG if you want to spend as low Dv as possible), I decided to keep going, and see if I actually could do it another way.
I usually use the flight plan @OhioBob described for any other planet : coming in polar, decouple the sats from the carrier, pick one sat and make it burn 'radial In' to make it pass on the other side of the planet, and then perform a capture burn for both sats.
WARNING : This path might not be optimized at all in terms of Dv, but i tried to see if I had enough to actually do something with this ship.
This time, i decided perform a little course correction (radially out) before encountering Jool. I came in quite equatorial, with a Periapsis close to 800.000 km. Then, I did a retro-burn (1300m/s) to enter orbit and i kept my Apoapsis as far as I could (things like 2.438.000 km). With that trajectory, I waited my Ap to do a inclination change. At Ap, it only took 328m/s, to reach 90° inclination. Then, i decoupled my sats, and did some fine tuning (1.5m/s) to get my Ap / Pe in front of the poles.
Last maneuver : burn retrograde till i hit Periapsis at 210.000 m with each sat.
They're now secured from any Joolian Moons encounter, as you can see :
Mission is now a success, with some Dv left ! Thanks for your help, and see you around ! I may post a thread for my next Jool / Eve mission. Stay tuned !