Welcome to the club.
I have an Amarok with a canopy, I use either an Altera Strada on the towball or a piece of 3/4 ply cut to size with a Kuat Dirtbag 15mm fork mount bolted to it.
I have a Bedrug in the back which with the ply being cut to size stops the whole thing moving, I also fitted two handles to the ply meaning the whole thing can be pulled halfway out onto the tailgate to make loading the bike easier. I found having the mount at the tailgate end the easiest way of loading.
I had a Ranger before my Amarok which had the ‘sports bar’ with side rails over the bed. I had a pair of roof bars over the bed and used Thule 591s to carry bikes over the bed. It took some mauling to get the longer bikes on where they wouldn’t catch the rear window but it was worth it. I could carry 5 bikes above the bed and two on the roof with a roofbox.