With the panel completed and in situ, I mark the centre of the hole. I take care to mark the hole at the top and not the bottom of the panel and this is important if you have selected grain for a particular aspect presentation. Establishing the distance between the two sides, I split the distance and this gives me the vertical centre-line . This then establishes the distance from the underside of the top crossrail. The two crossed lines mark the centre of the hole. Your hole size depends on the insert size of your chosen timepiece. I like to actually mark the circumference diameter onto the panel as a visual representation in the panel and I recommend this as it will help establish the size you want. If you hold the clock in the upright position to make sure you like what you see then you can cut freely. Also, the clock insert does not have to be as high or low as I suggest. You may want to alter that.
If you approve the position, cut out the hole. You can use a brace and expanding bit if you have one, or, as I did, you may want to use a coping saw threaded through a 1/4” hole. This means changing the orientation of the blade from time to time as you progress the cut around the hole. Simple!
You should check that the insert fits before glue up in case adjustment is needed.
Clamping is important even with tight joints as the thinner the glue the stronger the joint. Rehearse as many times as you want to make sure you are familiar with the assembly and equipment and so on.