This is what I do, really. Regarding styling I have a small styling script that I put after each graph. This small script takes the active figure (gcf) whatever it is, and changes it to my liking. So if I want to change the graph styling at a later stage I modify this small script and then re-run the main file.

But everything in MATLAB, then I just symlink the pdf figures to the manuscript folder, so with an F5 in MATLAB and a build in Sublime I have the manuscript updated.