It's not a tool setting, but a toolpath. When creating your toolpath, you want to define a sufficient "Chamfer Tip Offset" to push the tool lower in the direction of the part. If using a 90 degree tool, this is simple math to work out, as the maximum Tip Offset you should define is half the diameter of the tool, minus the chamfer width.
For example: a .125" x 90 chamfer tool can only drop .062" below the surface. If you were cutting a .01" chamfer and wanted to use the maximum amount of flute, you would define an Offset of .05" and a chamfer size of .01".
That said, most deburr/chamfer tools are not ground to a sharp tip (although they appear as such to the naked eye), so your effective tool length is often closer to .055"-.058"
Seth Madore
Customer Advocacy Manager - Manufacturing