So your problem is with the fitting plate, not the box right ?
If so, it really is easy. You should have two suppor tbrackets (big angle iron things bent through 90 degrees), a big flat metal plate with some nuts welded to it, a plastic thing with a load of diamond shapes in it and a flat plastic thing with a tiny hole at each corner. Oh, and a bag of bolts and stuff.
Right. Support the weight of the rear muguard (with one hand) and whip out the two bolts holding the grab handle on. Let mudguard down gently. Find the two long bolts in the bag and the two big, stepped spacers. Now find next logest pair of bolts, the plain looking spacers, the long thin spacers and the rubber washer things (both sets of bolts should have coutersunk heads i.e. cutaway like the tops of screws.)
Take the two long bolts, pass them through the holes in the big metal plate that line up with the ones where the grab rail used to be, then stick on a stepped spacer (under the plate) so that the spacer fills the hole in the rack. Place plate on the rack and loosely locate the long bolts in the mudguard holes (again where the grab rail bolts used to go).
Now get the next longest bolts and pass them through the other end of the metal plate. Slide the plain spacers between the metal plate and the rack (at the rear, where the slots in the rack are) using the rubber washers to protect the rack from the spacer. No nuts yet - don't worry.
Get your two bent metal support plates and determine left and right. The two holes line up with the pannier rail support holes, and the upper surface of the support goes inboard (i.e. you can only see the outer surface of the support from the side of the bike). Loosely fit these to the pannier rail holes (or behind the pannier rails if fitted).
Now slide a long spacer on each of the bots you left without nuts at the end of the rack - the spacer should sit between the underside of the rack and the top of the support bracket. Feed the bolts through the spacers, jiggle the support brackets until they go through them too and then put a Nylock nut on the end (with a washer).
Tighten things down starting with the most forward bolts (into the mudguard), then the support braket bots then finally the nuts and bolts at the back. Now you should have a metal plate bolted to the bike.
Now get the platic plate with all the diamond holes and place it on the metal plate. Line it up centrally and move it fore and aft until the holes in the metal plate can be seen through the diamonds. You might need to fix your top box to the plate temporarily and mark how much clearance you need from the rear seat - then whip the box off and align the plate. Some adjustment is available in the fittings but its pretty limited so opt for a whole hole furthe out if necessary.
Get the four diamond shaped washers and put one in each hole that lines up with a hole in the metal plate. You can have the slots fore/aft to give a bit of leeway, but I do one pair across and one pair fore/aft to eliminate play.
Stick the bolts through the washers and tighten. All that is left is to clip in the upper plastic surface (requires a bit of flexing and force) and then retain that with the tiddly screws, one at each corner. Sorted.
Sit back, drink beer and admire.
LC