Can I tie my exocage into real boatsides or should I just stick to mini boats (2x6 rectangle steel)?

yes you can, assuming you plan to tie the boatsides into a plated unibody

I have all my steel templates cut to plate the body. I was just wondering. I dont see any full boats with exocages when I did my research.. atleast not on XJ's

check pirate4x4. full boatside and exocages are few and far between on here