its very simple, select any layer which is free draw the shape of via, like rectangle to make box kind of via, circle to make cylinder kind of via, stright line to make planar via, (it is automatically extruded in to 3D by software), now go to subsrate create/modify, click layout layers tab, click the substrate layer in via you want to punch via, then on right you will find the drop down menu select the layer on which you made the shape of via, and click the button "via" which appear above apply button, thats it