You can package your INDD or INDB file. This will collect all files and copy them in a common folder, containing the INDB, all INDD and in a sub folder "Links" all related and placed files and in a folder "Document fonts" all fonts which have the permission to be copied into that folder. TypeKit fonts are not copied, as these have neither permission, but any CC subscriber will get them if they are missing automatically.
From now you should work only with files in the package.
If you late place an image, go to the Links Panel menu > Utilities > Copy Link(s) to… and copy these files immediately into the Links folder in the package.
I organize by client, creating folders for each client, with subfolders for various types of assets like logos and photos, then I link to the assets in those folders rather than making copies over and over.
…I'll have a lot of duplicate files from PS, LR, and Il…
Unless you think that you will have to change every instance of a particular graphic (like if a corporate logo that you use in many documents needs to be replaced with a new corporate logo), it's OK to have multiple copies, unless storage is an issue. I'd keep everything you need within a job folder, so it might be a folder for a client, a folder for each job for that client within, and in each job folder, an images folder and a fonts folder. If you aren't already doing it, make a PDF of the job when it finals, just in case you need to have something to tell you what the document looked like if the other files become corrupt.
I suggest you also make incremental copies of the InDesign document as the file develops.
And make copies of your files on an external device including off-site, in case your computer becomes corupt or is stolen etc. The off-line storage system that comes free with Creative Cloud seems excellent. Has anyone else used it and has views on it?
Not nearly enough storage and a bit too wonky at this stage. I'm sticking with Dropbox and OneDrive.
CC is fine if you want to share a layout with someone for review but I would not depend on it for backup purposes.
Thanks for your thoughts Bob.