I drilled the holes in the outboard bracket first. These pretty much set the lateral alignment although some adjustments can be made with the holes in the inboard bracket. So to get the pany aligned with the fuselage I used a couple large squares clamped together and aligned with the fuselage centerline.
With this big perfect square I could drop a plum bob from the tail and nose of the pant and see how far from the center line it was. Then I aligned the pant so it was the same distance on both fore and aft and drilled the holes in the bracket.