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.