Fortunately ChiliPeppr supports tool change.
Make sure you have your Tool Change position (G28) programmed on your machine first!
Fusion 360 will send the tool change command, and ChiliPeppr will pause sending.
The machine will move to this position. Then move it back to your work location
Then use the Z-axis probe feature to zero out your new tool (if you have it, otherwise by hand), and resume ChiliPeppr.
This description is a very light overview. I think there are a few forum topics and youtube videos about it.