When utilizing Hybrid operations (Additive and Subtractive), two independent pieces of software are utilized to generate toolpaths (Simplify3D for additive and Fusion360 for subtractive). So it is critical that the user ensure the coordinate systems match between the two setups.

For example, if you have an object that you would like to mill from printed stock, you may start from a CAD model such as this one:

Here, the green is the final part, the translucent is the printed stock, and the origin is in the center at the bottom. (The other parts are support and adhesion bodies, detailed in the Tutorial for this part)

The .STL files of the printed portions are exported from the CAD software (Fusion360 shown). When they are exported, they will utilize the model origin which is usually correct. Note: in Solidworks, this may not be the case, as SW gives the option to utilize a different coordinate system. Make sure you select the coordinate system you intend to  use and the Do not translate STL output data to positive space is selected:

In Simplify3D, ensure that the position of the model has not been adjusted:

In the preview, we can see that the coordinate system is still at the bottom center of the model:

Back in the CAM software (Fusion360 shown), select "Model origin" for the WCS origin in the Setup:

This will ensure that any toolpaths will be generated with respect to the origin used throughout this process.

Note: this is the simplest example of how to align coordinate systems between these softwares. There are other more complex methods for different setups, but the takeaway is always the same: the user must be aware of what coordinate system is used in each piece of software.