If your trailer doesn't sit level it will not distribute it's weight equally on both axles. This would likely result in overloading one axle. In your case, with the front high, you would probably overload the rear trailer axle and tires. Even if not overloaded you would likely have uneven tire wear.
You will need to either lower the truck or raise the trailer. There are plenty of people who have raised trailers so they can tow them with lifted trucks. If it's a really high profile FW you need to watch you're overall height and stay below 13'6".
The minimum bed rail clearance depends on how rough of terrain you plan on driving over. If it's all smooth pavement you can get buy with much less than if you're driving through a field or something.