Yep - use the bear boxes if provided. It will keep you out of official hassles if nothing else. Otherwise, the camper is usually fine, but we purposefully do not carry smelly food around. And if we want to cook fish, meat, etc. it is always outside on the fire or grill. Grill is then cleaned and stored in the cab. Some friends use a bear box as their receiver hitch storage box, heavy but effective. Especially good if someone rear ends you too.
The soft side issue seems somewhat up in the air. The FS regs on the campgrounds up by the Beartooth seemed to not allow soft sides at all, but friends said the campground host told them the pop-up camper was over 6' hardside and ok. Might depend on what campground host you get.