An organized work place is a good thing for both your creativity and your efficiency. The same goes for OmniGraffle. If you set up OmniGraffle the way you feel most comfortable, OmniGraffle won't be in your way.
The most common way of dealing with the program is to have the Canvas on the left side of your screen and then the palettes on your right, with the stencils on top, and the style palette below.
The problem with this way of setting up your workspace is that not only do you constantly need to expand and contract your style palette, but also that the two palettes fight each other for the same screen real estate. Even if you know the various shortcuts for accessing the various styles and stencils it is messy.
Perhaps a better way is to put the style palette to the left of the canvas, and leave the stencils on the right. This way you can expose all the styles, all the time, and have room for a lot of stencils on the screen at the same time.
However, you will loose space...