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You can align y-axis of both the charts so that the x-axis of both also gets aligned. This can be done by setting axis margin to top chart based on bounds of bottom chart.
chartTop.axisY[0].set("margin", (chartBottom.axisY[0].bounds.x2 - chartBottom.axisY[0].bounds.x1 - chartTop.axisY[0].bounds.x2 + 5));

Please take a look at this updated JSFiddle for an example on the same.

Vishwas R
Team CanvasJS