The way a multiplot graph is displaying scales is a bit curious.
It's true a graph displys all scales at the same time, so if the various Y scales are different the display is confusing as you said.
I suggest you some workarounds.
First of all, arrange all Y axis in order to have the same or multiple scale so that all grid lines are equally spaced.
Second, display the same lines for all Y scales (customizing the tabs as Alberto says).
Third, display grid lines for different Y axes with different colors (maybe choosing pastel colors for grid lines and the same but bright color for plots).
Fourth, hide all grid lines but one. It seems that this built-in option works in a curious way: if you have a black graph background you can see some pixels painted along X grid
lines where Y grid should lie, and if you have another color background you can see the complete but 'hided' grid lines, as if they were painted in black instead of transparent. So I suggest you to use for grid lines the same color as graph background : that way the Y axis grid lines are effectively hided.
Hope this helps
Roberto