How is primary fluid different from motor oil?

If your using Syn 3 oil nothing. The big difference between standard motor oil and primary/trans fluid is the lack of sulfur in the motor oil and the viscosity, the sulfur helps adsorb shock and is much better for the trans. A far as the primary goes the thinner oil is much better for your clutch, ATF is also a good primary fluid, many companies like Barnette recommend it.