Yeah I started doing that awhile ago. 1/6 boxes often waste volumes of space. Only recent sideshow figures optimize the packaging for space and storing.
What I do is take the accessories and wrap them in the extra mylar/plastic wrap that comes in the box, or I keep any small plastic bags from other things I buy. If they are delicate, I might separate them, but most often I can put multiple items, weapons, hand sculpts, etc in one bag. If they need extra padding, there's always bubble wrap. Headsculpts I would wrap and keep separately.
I put the figures wrapped in white cotton fabric, since that won't stain the figures in the long term. I wrap them in bubble wrap and put them in a custom made cardboard box. A glue gun and box cutters will be your best friends here. Accessories all wrapped goes in the box too. I've found it useful when I could make boxes and store 2 or 3 figures in the space a single Hot Toys figure would take.