I'm not that familiar with Mavlink and the mission planner, but can someone give me a head start on how to go about integrating the battery readings and viewing them in mission planner? 

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If you have a current sensor set up then this is already done.  Set the parameter for the (usable) capacity of your battery and Planner will show a % remaining based on the integrated current useage.  For example if you have a 2200 mAh battery and want to use 80% set the battery capacity parameter to 1760.  When you start the flight the capacity will show 100%.  When you have used 1000 mAh, the capacity will show 43%, etc.

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