Amanda technically isn't "real", or rather, she doesn't have a physical form. When Connor rendezvous with her it's basically contained within his consciousness, if that makes sense. Since Connor is an advanced Android working for CyberLife, he has immediate access to contact with Amanda who handles his work on pursuing the deviants, through I guess you could say their own exclusive network provided by CyberLife. As far as Amanda's origins go, if I remember correctly she was one of the first AI that Kamski designed, being modeled after his mentor. You can see a picture of them together in Kamski's apartment, though the Amanda in that picture is his mentor, and not the AI that Connor interacts with.
In the same vein, the garden that he meets Amanda in doesn't exist either, it's just a visualisation contained within Connor's consciousness that serves as their meeting point between his research. Whether it has any symbolic meaning, I'm not entirely sure, but it's a simulation that is at least capable of various weather effects as we witnessed with both rain, and later snow when Connor cuts his ties with CyberLife and Amanda entirely, should you choose to make him a deviant and he survives.