ginput might be what you're looking for.
Here's an example. Hopefully you can adapt it to do what you want.
xData = 11:20;
data1 = rand(1, 10);
data2 = rand(1, 10);
ax1 = subplot(2, 1, 1);
plot(xData,data1)
hold on
ax2 = subplot(2, 1, 2);
plot(xData,data2)
hold on
[x,y] = ginput(1); % get one input point
% plot and label that point in the first subplot
axes(ax1)
plot(x, y, 'ro')
text(x, y, [' x = ', num2str(x), 'y = ', num2str(y)])
% label that point in the second subuplot
axes(ax2)
plot(x, y, 'go')
text(x, y, [' x = ', num2str(x), 'y = ', num2str(y)])