Two Missions with different autopilots

I am planning to do a mission where I am using a drone and a rover. I want to make conditional command such that when a drone reaches a certain place, the rover should start working. So, how can I do that? and how can I put 2 missions in mission planer ?

Well, it needs some programming. Connect to the rover and copter in the same code (pymavlink or dronekit) and observe vehicle states. There is no out-of-the-box solution for this. You need to implement it.

Why do you want that?
You can also programmatically upload/download/configure the mission item lists on vehicles using pymavlink or Dronekit.