Is there a way to set a tool so it is the same orientation when it is loaded?
Rotate the model in the Tool>Preview. When it’s where you want it to be, press the Store button. When you save the model, the new orientation will also be saved. You can also get the same effect by using the Rotate deformation.
I’ve been meaning to ask this one too - is there also a way to save the tool’s scale, or redraw using a set scale ? Seems that markers are the only way to “save” a scale - if that’s the case can you save a marker ?
Your model’s scale has nothing to do with the canvas. By default, the model will be 1 ZBrush unit for a native object, and 8 for an imported object.
The fact that the model’s scale is independent of the canvas makes many other features possible. For example, you can draw a model on a small canvas (where it’s easy to work with) and place a marker. Then resize the canvas to the maximum and click the marker. The model will be drawn at the same size relative to the canvas without any drag on your system resources.
Ah, now that’s a cool trick. 
Thanks aurick!