There's sort of only 2ways of cover tyres covered on a tray back
A) make the tray super wide to cover them and turn the tray into a anchor point
B) keep the tray the same width as the body and run the guards out. It's no ideal if you have tray sides if you need to fold them all the way down, but still bets getting hung up on the tray
This is how I did mine


Notched out the sides to keep the tray low as practical
(Not the best pics showing how there done) but there's 7 bolts holding each guard on for a quick unbolt option on harder trips in tight tracks