Resilio and SyncThing both support different modes:
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“mirror” mode, where deletes on the source device are reflected on the destination device
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“send only” mode, where deletes on the source device are ignored.
You want the second option, so if your phone decides to “smart delete” photos that were backed up somewhere else, the backup on your NAS doesn’t synchronize those deletions.
If you’re using SyncThing, you want “send only” mode. If you’re using Resilio Sync, you want “Read Only-Full Sync” and “Store deleted files in folder archive” on the server folder (which should be set by default).
With respect to how I suggest people set up files, it’s up to you: I personally like to have my photos in one directory hierarchy, so I use automatic organization, but I’ve retained all my Resilio archives separately, as well (disk is cheap).
If you’d rather maintain a single copy of your photos and videos, you can either opt out of automatic library organization, or you can periodically archive your Resilio backup directory (take care to not delete the files that the app uses to maintain sync state, and realize you shouldn’t archive files on dest that still exist on src, as the sync app will re-transfer everything you just archived).