I have done the jig pocket, in a piece of plywood I use as a supplementary wasteboard that I bolt to the middle of my wasteboard using my 2 in grid pattern. I first saw the technique in one of John Clark’s videos.
I cut the plywood with enough extra to cover the holes I want to use then drill the bolt holes (with a pocket for the head) according to the grid of my wasteboard, (it can be done anywhere on your wasteboard);
I installed the supplementary wasteboard centered in the middle the main wasteboard using bolts;
Using the center position as the zero for creating the toolpaths, I pocketed the the supplementary wasteboard. Use the rapid position Center position in CC to place your zero as this is the repeatable position. The pocket needs to be a thou or two bibber than the part to make it possible to insert into the pocket but tight enough to prevent any movement.
Like your supplementary wasteboard, design your toolpaths for your part with the center as the Zero point for your toolpaths. Set your part in the jig, zero the machine at the center position and mill your part. Even if it is inside the pocket, make sure your part is secure using double sided tape and or clamps too.