I drill out lots of these holes, and the process is simple. Start with the largest diameter bit, then when done, move to the next smaller size and drill further, using the center point remaining from the first bit.
But what happens when you need to drill the shoulder, after the smaller hole is already there? If you’ve tried it, you know that the bit will wander mercilessly when you try to start.
My solution? Use a second block of wood as a guide. Drill the larger hole through the second block all the way. Now, center the hole in the second block on the first hole in the original piece. Clamp the blocks together. Now you should be able to use the second block’s hole the capture the bit, and guide the starting cut into the original!