I setup one for a client that could access two subnets in Amazon. I'm pretty sure I did this by adding a static route on the vMX to the second subnet and saying to include that in AutoVPN.
However when I go to look at it now I can't get to the section where you can add static routes. The route table does show both of the subnets used by the client in Amazon AWS.
So now I'm not sure. Either it used to allow static routes and doesn't now, or - well I really can't think of any other option.