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When running the backup software "Back in Time" on Linux as a normal user is no problem at all. However you will be limited to the directories and files that you can back up that are accessible as that normal user. If you want to back up things only root can access then you'll need to run Back in Time as root. There is a mode to do this, however there is a bug with the scheduling code which sets the cronjob as root to run the backups. This can be corrected by manually editing root's crontab after you've set up Back in Time as you want. Set the cronjob to look something like this:

#Back In Time system entry, this will be edited by the gui:
0 1 * * * /usr/bin/nice -n 19 /usr/bin/ionice -c2 -n7 /usr/bin/backintime --backup-job --config /home/schristensen/.config/backintime/config --profile profile1 >/dev/null 2>&1

Update: with recent changes to backintime, the cronjob should look like this now:

#Back In Time system entry, this will be edited by the gui:
0 1 * * * /usr/bin/nice -n 19 /usr/bin/ionice -c2 -n7 /usr/bin/backintime --config /home/schristensen/.config/backintime/config --profile-id 1 backup-job >> /root/backintime.log 2>&1