Hello Darkith,
It looks like you have hit the nail on the head here.Using a seperate battery to each board may cause additional unwanted problems.I think I'm very close to fully understanding what you are trying to explain to me.(I'm a monkey see,monkey do type of guy-LOL).If I use two batterys on a Y-connector going to the first board,hot leg to its normal mounting position and ground to its normal mounting position on the board.Then tought I would run a jumper wire from hot leg on first board to hot side of second board.Same for ground,Jumper from ground on first board to second board.This will insure power to both boards being equal.
Hope the way I wrote this so far makes sense.
But one more time if I go this route,in your opinion can I make up a Y-connector for the three wire plug and connect the little board to both big boards.Or even in this case the one wire still must not be used on one of the boards.
BIGMIG