Doctor Who 2 (4/5/2015)
I've used SSMS mostly and prefer it. I've not really used SSDT all that much. Can you do things like create SQL Jobs in SSDT?
Technically, I see no reason why you couldn't run sp_add_job from SSDT, but that's probably not what you had in mind.
There seems to be no capability to include Agent jobs in database projects, but that makes sense, as they are not related to any user database.