This feature pertains to the part file you are working with rather than the general system settings of BobCAM. It is the same as the Settings Default dialog box, only without file path options. Making changes to this feature only affects the part.
Toolpath - This allows you to select the default color for new toolpaths created inside of the current part file.
System - This value sets the tolerance for the calculation of toolpaths.
Chain Select - This value indicates the largest distance between two entities that is acceptable when selecting a chain for toolpath boundary containment.