You can always glue the seal to the cap and not the bed. I glued it to the bed simply because it's easier, but have gone the other way around in the past.
Also, I needed to use a thicker piece on the front bed panel. My Jeep caps front flange is a bit higher than the side flanges.
1971 Gladiator J2000 Platform-Stake Dump 350/T18
1970 Gladiator J3000 3407Z Camper Truck 350/T18
1968 Gladiator J3000 3406Z 160" wheel base DRW 350/T18
1963 Gladiator J300 Townside 350/TH400