Best corporate structure for two separate but symbiotic B2B entities?

There are 2 symbiotic start-ups, a B2B manufacturer and a B2B software developer/provider, where the later makes software specific to factory operations in the manufacturer’s industry. Both must work together in the early stages, share resources and are inherently tied together in terms of initial business development. The challenge is that when the software provider branches off to sell its wares to businesses, it will sometimes be selling software to competing manufacturers, and thus it needs to be distanced from its manufacturer partner once both businesses are fully operational. Accordingly, given legal, ethical and financial factors, what’s the best way to organize these two business entities such that overall management control is maintained over both and…