Are you build traditional bus system or two independent systems connected serialy by any protocol?

When you use a full parallel bus with port adressing, then you can add central bus clock quartz stabilized on Master Board,(Example ISA Bus in old PC).
Use X1 input of both uPC inputs and work as external Clock. It give you fast communication beetwen uPCs. Two iPC will work synchronicaly at the same clock, but don't disturb one another.
and communitation will simply and as fast as it posible.

But when you use a serial connection betwen uPC, You can make two independent clocks. But amount of transmited data must be short or speed of transmission low (I think abaut asynchronic transmistion) or you can use calculation of CRC etc..

So it depends of speed of application, speed, used protocols.