In a nutshell I only shoot RAW photos and download all of them to a NAS device that is being watched by Amazon photos. Whenever I add a new folder or photos to the watched directory on the NAS drive it uploads them to Amazon and maintains the directory sturcture, I try to name my directories by location and date for the NEF files, when I upload to SmugMug galleries they might get sorted a bit different but I try to include the date in the gallery name there as well.
Hope that helps.
Looks like I will need to incorporate a NAS device.
Thank you!