I really like to carve out hold downs that match the screw placement in the waste board. What I do is cut the stock slightly larger than needed for the piece. When designing the piece I will start with a grid pattern file that matches the threaded inserts in my waste board. See the image below. This is setup so that it is ready to carve out any of the holes I leave behind. The smaller inner hole goes all the way through or very close to the bottom of the material and the larger hole goes in about .35 inches. This allows the bolts I use to end up below the surface.
I draw a shape around the circles the same size as the board. Then I would design what I expect the final shape of the piece to be. This shows me which circles will be within the full board but outside the final piece. I would delete all the circles that are within the final piece or outside the board and leave me only with usually 4-6 holes to hold the part down while carving. An example of this is the cribbage board I am designing below. The two sets of circles on the far left and right are for my hold downs.
Once I have the basic design and holes determined I will group the whole thing and centre it since I work from center usually. Once they are centred so the hold downs and parts have not moved in relation to each other but have centred on the project I ungroup them again. As you can also see above I will then also configure a box around the entire board to allow me to surface it with a surfacing bit so it is all flat in relation to the router.
Once I start carving I will clamp down the board in places where my hold down holes are not going to be and set the retract height to .5 inches. This means as the CNC cuts out the holes it will go over the clamps I have. I set zero to the centre of the board and carve out the holes. Once those are done I take off the clamps and then I bolt the board directly to the waste board using the new holes since they line up perfectly with the threaded inserts.
I then re-centre Carbide Motion and run set my retract height to something much smaller since nothing will be in the way now. I usually go for around 0.1 inches. The bolt heads are below the surface and outside anything I plan to carve. I run a surfacing pass and then will run the final project. I like to keep the surfacing as a separate nc file since I have had some boards that needed more than one pass so I will re-zero the z axis and just run it again if the material needs it before I start the actual project.
I know this sounds more complicated than what you are doing but it has served me very well when it comes to making sure my work holding is out of the way and the boards are flat and ready for carving. It took me a fair bit of trial and error but this seems to provide me with a very consistent work holding solution that I know I can trust.
Here is an example of it in action.