I am not sure I understand your issue. You just have to move 2 H-atoms such that they are separated by their equilibrium separation distance, e.g., you may use experimental value as an initial guess, and then do geometry optimization using some of the available DFT methods. You can always measure the distance using the Measure tools in the Builder/Viewer to measure this distance. For example, put one H-atoms at the origin and the second one along x or y, or z axis of the cubic unit cell. Then you can set the position of this second atom according to the separation distance of H2-molecule.
