The indictment suggests to me that Manafort hired Co. A and Co. B to lobby Congress. I believe that the indictment claims that at least Co. A may not have known about the foreign Yanukovych(Putin)/Party of Regions entity, The Centre, implying that Manafort hid that information about Russian-Ukrainian lobbying from Co. A.
I could be wrong. When I get time later today, I'll have to read it again to verify that.
My superficial reading/knowledge indicates that the PG and Manafort have had multiple interactions over the years with various org chart reporting relationships not all of which may have been well documented.