The double sided PCB’s are helped out by the camera, you basically find two drill holes, align the camera to one, find the drill hole that matches on the gerber , centre the cursor on that , right click and it moves the Gerber’s to match, second hole does the rotation.
Drill Test, trying different depths with the V90 bit, the software has a couple of extra modes to help get rid of the bits that come loose if different drill paths are too close, one is an extra isolation remove. This one I haven’t tried yet, it cuts away a little extra isolation to help with potential shorts, the second mode is rubout, you define a rectangle in the mech layer, or in PhCNC and the software calculates which areas to remove leaving just the tracks, this is heavy on the drill bit usage and takes a lot longer, you end up changing tools maybe 3 or 4 times. The good thing is you can try out nearly everything the machine can do with the demo version of PhCNC (Except camera), it does a cut simulation too. http://www.accuratecnc.com/download.html
Not deep enough, These next images are after the double sided cut , checking alignment, the blue areas are the drill path, the black is the copper left, as you can see they match up pretty good.
Find and align the first drill hole. I just did a rough guess watching where on the PCB the camera was and then used X<> Y<> to find it, make sure you focus the camera first
Then just match up the red circles as close as possible.