Cathy...I have my girls in totes with clothes and other little items in separate boxes. I now need to get the girls to separate into which belongs to which so they can take home and decide what to do!
An over the door shoe holder works well.
My dad made me a Barbie carry case and separate cedar chest for all the bits and pieces. They sell them in the "pink" aisle of any toy section. You can easily make your own with shoe boxes, contact paper, mod podge. Tons and tons of ideas on Pinterest too.
I would use a wood chest. Easily accessible at any age. On the inside of the lid screw plastic spice jar holders, spaced apart to accommodate the dolls. They can easily be snapped in and out at the dolls waist. Depending on your child's age, use ziploc bags to store all the clothes and accessories. And plastic bins for the larger items.
I still have all of my daughter's American girl dolls stored in the basement. I have them in in clear plastic bins. I have them labeled with what is inside and stacked on wooden IKEA shelves in my basement. Everything is organized and easy to find. They stay clean and they are easy to clean up.