Clay works by the principle of ion exchange. Clay mineral structure is such that it attracts toxins from inside the body and literally pulls it out from the body so that these toxins are absorbed into the clay structure where they are tightly bound. As for the clay minerals getting inside the body, it is a lesser degree than the pull of the toxins out of the body. However, if you take clay internally, the minerals in clay are absorbed by the body while at the same time, toxins are removed from the various organs and into the clay. Ultimately, the clay is excreted by your bowel movements.
One thing that I do to increase absorption of clay minerals by my body is to prepare my clay with shilajit or fulvic acid in a solution overnight. The fulvic acid or shilajit (which contains fulvic acid) will transform the minerals into ionic forms that is more absorbable by the body. Search google for "fulvic acid minerals" and start reading.