Hey Tony, I have been playing around with different methods to do inlays. For shallower inlays I use Estlcam and set the starting depth for the plug lower (there is a thread around somewhere on how to do it), for deeper inlays I use F-Engrave. I had the same problem you have in the beginning where I had two V-Carves that had to be done separately because it was a two-colour inlay. I cut the negative with Estlcam using two layers and the plug with F-Engrave. That worked surprisingly well. 
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