I am using ubuntu server running gitlab server.
I need to perform daily backup/restore of my gitlab.
Which method should I prefer: omnibus or from source?
How can I check weather GitLab is installed via omnibus or from source?
Source or Omnibus, you will have access to the same backup procedure, which will create an archive file that contains the database, all repositories and all attachments.
That means you are saving the data itself, not the all system.
For the system, note the version of the omnibus package you are installing, and you will be able to re-install it in minutes.
How can I check weather GitLab is installed via omnibus or from source?
See if your gitlab root folder has a .git in it: that would mean it represents a clone from the sources.