Is there any way to run two inputs for different apps? e.g. when in a game called minetest you can run a local server and setup a dual player but not dual controls.
No, however, multiple mice can be used.
This can be done with two, or more?, mice using Peter Hutterer's MPX which is now included in Ubuntu's xserver which requires some setup to configure your xinput devices.
What you're after, having two different sets of input devices cannot be done, easily. The main issue here is having an "active window" which means all input can only go into that one window.
There have been some research projects in the HCI field around this area, creating multiple active windows for multi-user environments with varying success. But as it stands there isn't really much available for us humble users to play around with.
