I do this a lot… I too have a jointer and a planer, but the CNC is so much better at getting a precise thickness. Of course, very few boards are dead flat, they can be cupped, bowed, or twisted. So i find the side with the least amount of movement when placed on a surface and put that side down. I use masking tape and CA glue to secure it to the wasteboard, making sure to get some contact between the board and the wasteboard. Hot glue works as well.
I use note papers to shim the corners or middle where it’s not laying perfectly flat on the table. Strips of note paper is nice because you can fold it in half, thirds, quarters, etc until you’ve got the board stable. It’s important to make sure the board can’t move vertically because it will get pushed by the bit and you’ll end up with a board that’s not flat. Take a pencil and put lines across your board every inch or so from edge to edge (closer for smaller pieces). Now run a leveling toolpath on the board. The pencil marks will make it easier to see your low spots.
Now, drop the endmill to the zero (+6mm) and then drop it to it’s actual zero. Then you can lower the endmill a little more (this is a guess, depending on how curved the surface is). Run the leveling program again, check your reference marks, maybe re-zero and run again (and again… and again) until there are no more reference marks.
Flip the material and you should have a board dead flat on one side, although most definitely not parallel to the other side. Attach it to the wasteboard, and mark your reference lines. I like to run the leveling toolpath again with the same zero because of the warp and shims, I’ve been surprised by the high points. Then repeat the lower zero - leveling toolpath until your reference lines are eliminated, and you have a board with parallel faces.
One thing I like to do when figuring out my initial zero is to zero off the wasteboard, then raise the endmill by a known amount, say 3/4" for regular 1" board, maybe a little more based on how much the board is warped. Then I take notes so I remember where I am and will have a record of the final thickness for setting up my jobs. For example, with a 0.02" leveling toolpath, I’d have notes like this: