I have often been confused by this and every time I have to redo my configuration I have to re learn. I find the best way to use it is start from the Marketplace/Smarttapps/Smart Lights. From there select what you want to control, ten what you want to do and from the how you want to trigger the action select the button controller. I hope this helps.
The native device handler is working. You just can’t use the individual button devices you must use the device itself and then choose a button. You can no longer remove the minimotes through the mobile app. You have to go to the IDE and delete the device. When you try to do it from the mobile app it says it removed a different device and there is no way to then remove it through the interface. Obviously still a work in progress. I have notified support on the interface bug.