If CAMWorks 2016 creates my turn setup on the wrong side of my part, how do I flip it?

When you open a turning part, CAMWorks will automatically locate the smallest end of the part to be machined first.  

If this is not the orientation you want to machine your part in, you will need to add a coordinate system on the end you wish to place the new origin location.

Once the coordinate system is created, ensure that you choose this coordinate in the setup tab within the machine parameters.

Once the new coordinate it set up, you can run extract machinable features, or add in your new part setup manually.  After the Turn Setup is created, you will need to switch to the Operation Tree and Edit the Definition on the Turn Setup.  Switch to the Origin tab and select Automatic as the location in which the Origin is Defined from.  This will automatically move the origin to the correct position in order to get the desired GCode for your turn program.