not sure what a cmd pack is, so i'm not entirely sure what the problem could be, but to explain the new limitation with item models, it's that all of the textures for a given item model must come from either just the block atlas or just the item atlas (it can't have textures from both).
assets/minecraft/atlases has files defining which textures go in which atlases. for simplicity's sake, the easiest way to make sure a texture goes onto the correct atlas is to put it in the corresponding texture folder (so, if you wanted a texture to go onto the block atlas, you would put it in the block folder).
