I did read the original Installation material... I was getting stuck on the PHP stuff.
I ended up going with Nextcloud, which I admit I didn't even know was a thing.
I live the web interface, but the PC client leaves a lot to be desired.
Can't keep several folder sync'd at the same time and no way to select how long in between syncs.
So Im guessing the way to accomplish what I want is to have separate sync for every folder I want sync'd? I was under the impression that the software was able to keep better records of what goes where. I will try that tomorrow...
If you use a "big" folder to sync everything, everything will be inside of a single folder at the Nextcloud server side. However organized as the original folder inside it. Nexcloud keep track of the sync using some hidden files inside the folders.