Controlling it with a spare arduino seems the best way to go. Put thermistors on each bed and slowly heat them up until they are within a couple degrees of each other. It wouldn’t be hard to use a rotary encoder to change the temp setting and have a small Hitachi HD44780 based display read out the set value and the temperatures of each bed. On the slicing side, just set it up like there is no heated bed. Doing that might change a few of the more advanced settings, but I don’t think that should really be an issue. Just heat the beds up before starting the print with the ramps board.
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