The most common problem with the software not asking for a tool is the post processor. Every CAD program, Vetric/CC, has a post processor which incorporates your accessories like BitSetter and BitRunner. Vetric has a Shapeoko post processor which supports the BitSetter. When you create gcode without the Shapeoko post processor the generic gcode is not aware of the BitSetter and the ability to run jobs with multiple tools.
Check out this post:
The user Neil is a guru for writing post processors. The above post is from 2020 so it may not be the most current one for vetric.
I dont use Vetric but the Vetric forum and likely here on the forum tells you where to select and place the post processor.