That sounds like a really good combination and the story hook of rescuing your last hero is a great framing device. I hope it turns out the way you want it to.
The parallax effect looks great when you're zoomed in, so you could have most of the game play with the camera close to the player character. For the later parts when you're controlling an army and need to see more, zoom out the camera and move the parallax layers closer together. This sort of approach should reduce the distortion at screen edges.