Partially covered in this discussion, at least the way some of us do it.
This depends on what HW you have (BitSetter or not), what G-code sender you are using, and what post-processor you are using in F360.
If you have a BitSetter, see here for an example of using Fusion360 to generate a single G-code file with all toolpaths, that will handle the tool changes (M6 commands, that CM or other senders will recognize).
If you don’t, you need to do it the same way you would in Carbide Create without a BitSetter, i.e. generate one G-code file per [set of consecutive toolpaths that use the same tool] and run them separately.
You can just select one (or several) specific toolpath in Fusion360 setup, and click the post process tool, it will generate G-code for those toolpaths.