That's a nice set-up. Having the stake pockets seems to make it easier.
Most people with Gladiators seem to end up buying a tonneau with the t-slots and mounting racks to the top of that. There's some nice DIY options using extruded aluminum by different users on this forum. I did worry about all those bolts loosening after lots of bumps and washboards. And I wanted a middle-layer rack right above the tonneau, too.
I went with Voodoo VRS rails (mount to trail rails), put a roll-n-lock XT tonneau on top of and had a welder weld up an aluminum c-channel rack that matched the angle of the truck and the height of the softop. That also allowed me to put a extruded aluminum middle-layer rack an inch above the tonneau to hold the cooler and other stuff above the tonneau but below the adjustable canoe rack up top. Works pretty good. It's all powder coated black now and has more 80/20 on the sides for other things.