Apologies, the link I gave didn't really explain what I meant.
The joysticks you use will be the deciding factor in whether you need to top or bottom mount them.
Happ supers have a height of 87mm from the mounting plate to the top of the bat and can easily be bottom mounted. Mounting them to 18mm (3/4") MDF etc will give you an effective height of 69mm (minus 3mm or so if you are using an acrylic top). You can increase the height by routing out material from the bottom of the CP up to about 12mm thickness as you said which would give you a maximum effective height of 77mm.
If you are using something like the Sanwa JLF or JLW (U360) you will need to top mount them as Japanese joysticks are traditionally mounted to thin metal CPs. The JLFs have a height of 69mm (using a 35mm ball), the JLWs (U360s) are even less at 62mm. Even if you router out the CP base to 12mm thick you will be left with a stick height of 50-57mm (minus 3mm again for acrylic if you are using it). IMO joysicks heights such as these are too short to be used comfortably and you will need to top mount them.
To top mount them you cut a hole straight through the CP for the lower joystick case to slide though. You then counterbore/recess the top of the CP for the mounting plate to sit in so that it is flush or just below the CP top. You may need to increase the depth of the recess depending on what mounting hardware you are using.
To top mount the joysticks in this way you will need a drill, jigsaw, router, pattern bit and flush trim bit (optional). You will also need somew small scrap pieces of MDF to make some routing templates for the method that I am going to use.
A pattern bit is similar to a flush trim bit but the bearing is at the top of the cutting flutes:
The pattern bit will be used to counterbore the recess in the top of the CP.
I'm hoping to start on some CPs when I get home today so I should have some pictures up in a day or so.