Well I will tell you how I did mine, but that doesn't mean it is the only way. I too have a MLC arena JP and a Seeker harness.
I first mounted my back armor to the vest in its final location. Then I used a sharpie to mark where the slots in the back armor landed on the vest. Using a sharp razor I cut the slots enough to allow the straps and clips to pass through them and the backplate.
For the JP I cut two slots just above the opening of the door with a dremel cutoff wheel and small files for cleanup. I would have liked to put them lower so that the JP would have riden higher on my backplate, but I was afraid to get too close to the opening of the JP and cause the fiberglass to crack. Using the other straps that came with my Seeker harness I stuck the non-clipped end down through the opening I had created and looped them around the two metal rings inside the JP. I pulled them tight on the inside so that only the clips were left outside the JP and secured the ends with chicago screws.
As far as the JP door goes I drilled a hole in each corner through the door and JP. I then glued in some nylon threaded nuts to the inside of the JP. I could then put the door on and screw a nylon screw into each corner to hold it in place. I used nylon so that it wouldn't scratch the backplate as bad as metal.
I hope that helps. Let me know if you have any questions.