How to Backup: Deja Dup + which application?

Yes, you can.
Open Backups Deja Dup
Click the "Folders To Save" option in the left hand pane.
Click the "add" (+) button toward the bottom.
Select "Other locations" from the left pane.
Select "computer"
Select the folders / directories /files you wish to include in the back up.

As far as other options go- In reality everyone has an opinion and a preference. Sometimes the best way to find yours is by exploring and doing.

Be Warned:
When you save a back up of directories in Root, it is possible to also unintentionally back up a problem. Often, when users make a back up, it is to have a way of restoring personal files if installations in root go nutso.
Unless you have some very tedious and tricky installations you are wanting to never go through the hassle of doing again, it is often easier to install fresh (With configs saved in HOME) and install them again than it is to try to back them up.

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