Alex, not sure I follow your question, but try this. Make sure you position your drawing over X0 Y0 in BobCAD. The CAM side will key off of the axes for position, so if you draw them "way out in space", you better have a big table to take that in to account!
For the Z axis, you define the heights in the CAM tool you right. Inside the tool (pocket, Z level, whatever 2 or 3D tool you select), you choose the Material Height in the first setting. You don't have to follow the model on this one. If you want to set the top of your part at 0, select 0 here. If you want it to be at 1" on the mill, put in 1. Also select the clearance from that height for your rapids - this could be important if you are using clamps, but usually I just use .1" to clear the part.
Finally, when on your mill, you need to set the tool at 0,0,0 on the part (with respect to what you entered in BobCAD), and rezero all axes. Then you should ALSO (in my experience) select "Ref All Home", and rezero them again. If you don't do that, you might find the tool diving in to the material! (don't ask how I know).
Hope that is enough to get you moving along, post up further questions if needed.