I don't entirely understand what you want to do, but this may be part of the answer. Using an example from the documentation:
figure(32767)
Z = magic(5);
h = bar3(Z);
colormap cool
colorbar
[az0 el0] = view % Find current orientation of figure
then experiment with view until you get the result you want:
figure(65535)
Z = magic(5);
h = bar3(Z);
colormap cool
colorbar
view([-10 60]) % Set new figure orientation
There may be other ways to do this, but this is the one I'm familiar with. You can also do it interactively in the plot window until you get orientation you like, then read the resulting [az el] values to incorporate into your code.
I'm sure you've already seen this documentation (core MATLAB), but Bar and Area Graphs may answer some of your other questions.