Been there, done that. I used to level the bed, make special fixtures for the PCB, use double-sided tape, masking tape, silicone, some special glue ($10 a bottle)...
None of that was worth the hassle. Trying to mount a PCB perfectly flat and level is a useless exercise in futility. If you look at commercial prototyping machines such as LPKF, you will see that they are not relying on the PCB being flat. They are using springs and adjustable rings to control the depth of cut.
Another option - probably the easiest for a hobby machine - is probing the surface with software like AutoLeveller. It works amazingly well even with severely warped boards. So I just mount the PCB any way I like and let the software do its magic.