I'm sure rubjonny will come along with the correct answer but.....
afaik it's a matter of fitting the alignment tool, then undoing the pinch bolt on the end of the rod coming from the gear lever..
there's a marking on it where it should be to have it all lined up properly so you can adjust it to that and tighten the bolt back up again. Obviously if this doesn't work and you didn't have the linkage replaced when the box was fitted it may be a case of replacing all of that to get it working properly again.