Phase is term used when you have VTL setup in your system. The phase1 is from client to VTL(which is can be a server with higher disk capacity or dedicated VTL hardware) , phase2 is from VTL to tape-drive.
You are correct in theory, but just to clarify, Phases of the job, in this case Phase 1 and Phase 2 is just the difference between the BACKUP and the DUPLICATION or DATACOPY. So, Phase 1 will always be the backup, and Phase 2 will always be either the Duplication or Datacopy to ANY type of target. It can be Disk to Disk or Disk to Tape, even Tape to Disk, not solely from VTL to tape.
And yes, instance is just the number of times the instance of that job has ran.
So if you see for example, Job ID 42 (Instance 12) that means that job has ran 12 times.