I would like to create a project contains 6 servo motors and Arduino Due board, but I have no idea how to operate should I use only a 9V battery only or in addition to 4 AAA battery?
closed as unclear what you're asking by gre_gor, user31481, per1234, jfpoilpret, dhimaspw Feb 6 '18 at 3:57
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There is no best way in general. With your setup you may use a 9V battery as input for the Due (over the power jack, which wants voltage between 7V and 12V) and using a voltage regulator to get maybe 6V from your 9V battery voltage for your servos. Make sure, you get a regulator that can give you enough current for the 6 servos (You can find this info in the datasheet of the servo motors).
Of course you can also drive your project with 2 different battery packages, like you have described it in your question. Note, that you have to connect both grounds to make this work.