Hi Ruben:
Yoni mudra can be practiced either before or after meditation and samyama. In the lessons, it is first instructed to be done before meditation. When chin pump is added, yoni mudra can be shifted to be after meditation and samyama to avoid doing too much energetic practice before meditation. It is the practitioner's choice. Do what works best for you.
Note: There is also the alternative "yoni spinal breathing" practice referred to in CarsonZi's post above.
All the best!
The guru is in you.