Two-phase, vertical nanocomposite heteroepitaxial films hold great promise for (multi)functional device applications. In order to achieve practical devices, a number of hurdles need to be overcome, including the creation of ordered structures (and their formation on a large scale), achieving different combinations of materials and control of strain coupling between the phases. Here we demonstrate major advances on all these fronts: remarkable spontaneously ordered structures were produced in newly predicted compositions, vertical strain was proven to dominate the strain state in films above 20 nm thickness and strain manipulation was demonstrated by selection of phases with the appropriate elastic moduli. The work opens up a new avenue for strain control in relatively thick films and also promises new forms of ordered nanostructures for multifunctional applications.