The pockets on the back are no secret and a pretty straight forward process. When I'm cutting out the design I normally use a 1/4" end mill and use tabs. The hole where the stem will protrude is usually a separate cut file that's the size of the stem that I cut completely through the material. When it's cut, try fitting the stem into the hole. If not, enlarge it slightly.
When I'm finished with the top, and before I separate it from the tabs, I flip it over exposing the hole on the backside. I set the project back on the table, run the 1/4" end mill down through the hole to square up the project, clamp, and cut a pocket about 3/16" larger than the clock mechanism and the depth to allow it to sit flush.
The depth of the pocket depends on the thickness of the mechanism you're using. The hardest part, if you want to keep it flush with the back, is figuring out if your material is thick enough. You need to add the thickness of the mechanism then allow for the depth of cut on the front, if you're doing 3D, and buy the mechanism with the right length stem or you have to change the depth of cut on the front.
These little clock mechanism come with different length stems and you can pick them up at most hobby stores for about $5. I have several in different sizes and get mine from Clockit.
You can turn literally any project into a clock. I hope some of this made sense.