If you have a BitSetter and it’s enabled, it should be taken care of automatically by the workflow. If you do have a BitSetter, it’s enabled, but upon the tool change the router stays down after the end of the pocket clearing phase, chances are you selected the wrong post-processor (it should be “Carbide3d Shapeoko”, not “Basic G-code” or “GRBL”)
If you don’t have a BitSetter, using Advanced V-carve toolpaths is not readily supported, but there are workarounds (see this post for example)