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1. Try placing a point (from ref geometry) in the centre of the cylinder end and one in the centre of the cube side in the part files, then mate them together in the assembly. You can also use a sketch point to do the same thing if you wish. You would also need to mate a plane of the cylinder to a side of the cube to stop it turning.
2. You could also create the cylinder in the assembly using the cube side face as the sketch plane and locate your sketch as needed to the cube face
You can mate sketch entities or planes like Front - in the assy find your parts and drill down to the appropriate item right click and Show. N.B. Make sure that you have enabled viewing of
them in the View menu on the main toolbar. Use them as selectable items.