It seems that you are doing your backups manually. A more efficient way is a backup program. For Gnome I recommend deja-dup: it’s well integrated into Gnome and after the first configuration of your backups, deja-dup runs automatically if you want. In the Fedora repositories are much more backup programs where you can choose what you want to use.
Yes you can. However, make sure you include hidden files and folders for both the backup and restore process (they contain all your configs). To show you all hidden files in folders in Nautilus (file manager), press CTRL+h.
Rsync is a good tool to use for manual (or even scripted) backups as it:
Does not copy files that have not changed since the last time copied
Copies everything under the directory selected, including hidden files and directories
Copies and restores exactly what is current at the time run.
Is able to delete files on either end that do not exist on both so that the overall file systems remain in sync.
Rsync also will not replace nor overwrite files that are newer on the destination than on the source unless explicitly told to.
If you continue to do the backups manually rsync is much faster and easier than using cp.
The file manager uses (I think) cp so you are stuck with its limitations. To copy the directories simply select the directory at the source and copy (either with ctrl-C or with the mouse) then select the destination and paste it (either with ctrl-V or with the mouse). It will ask if you want it to merge the directory and skip or overwrite files as normal. Note that the file manager does not look to see if files have changed, only that they do or do not exist.