Well to answer part of my own question, I found out how to plot with plotyy, but still have no clue how to add the error bars. Here is the new code:
sliceNum = 10;
figure
ax = gca;
for x = 1:sliceNum+1
s(x) = struct('field1',rand(1,5)*10,'field2',rand(1,5)*10+40,'field3',rand(1,5)*10);
end
needed = s(2:end);
nums = reshape([needed.field2]',5,sliceNum);
cal = [40 0.8 0.9];%need to find source
AreaVal = nums(1,:).*cal(1);
meanVal = nums(2,:).*cal(2);
RMSVal = nums(3,:).*cal(3);
numsStd = reshape([needed.field3]',5,sliceNum);
AreaValStd = numsStd(1,:).*cal(1)*0.05;
meanValStd = numsStd(2,:).*cal(2)*0.05;
RMSValStd = numsStd(3,:).*cal(3)*0.05;
[AX,H1,H2] = plotyy(1:sliceNum,AreaVal,1:sliceNum,[meanVal; RMSVal],'plot');
set(get(AX(1),'Ylabel'),'String','Area')
set(get(AX(2),'Ylabel'),'String','Mean and RMS')
set(get(AX(1),'Xlabel'),'String','Slice Number');
set(H2,'LineStyle','--')
legend(AX(1),'Area','Location','best')
legend(AX(2),'Mean', 'RMS','Location','best')