It varies. I did the same thing, for a different reason; I'm finishing my MS now and beginning my PhD next fall at a different university.
Indirectly, doing the MS has benefited me by allowing me to improve my PGRE score, get a lot more research experience, and show that I can do well in graduate classes.
Directly, the benefits vary from school to school. Some have told me that I could take the qual right away and, if I pass, be exempted from any classes. Others have said that I will have to take all the courses again because they don't really accept transfer credit. It really depends on the school.