What nynaevelan said should work. Make sure that any personal documents are in exactly the same location with exactly the same name including capitalization etc... I'm unsure of what the Amazon backup of your collections does regarding personal document locations. It won't backup the documents themselves but I don't know whether it will backup the personal document collections.
The alternative is to use one of the utilities which help you organise your collection from your computer. It is significantly easier to create/recreate your collections this way than to tap tap tap on the Kindle itself.
Kindelabra: Kindle Collection Manager and
Kindle Collection Manager for Windows are the two on this forum. I've no idea if there are any others out there.