Because the Amiga has so many smaller sized files, I find the easiest way to back up is create an lha archive of each individual top level directory on the Amiga drive and then copy these to my NAS.
That way if you have a directory that does not change you don't need to create the lha or copy it to the NAS each time. It also makes sure all Amiga file attributes are preserved.
Syntax to backup Libs folder, for example, (that I have copied from other members here I'm sure, is);
lha -aerzx a Backup:Libs.lha Libs/#?
Assigning Backup: to a folder on your Amiga drive is faster than running it over the network, and then copy to NAS after all the lha have been created.