I think Marcone uses Harry, but does not manipulate Harry. If he got Harry to do things he otherwise would not do, then you have a case for manipulation. But mostly Marcone sees Harry as a useful club against his own personal enemies. It is that "I use my enemy to destroy my greater enemy" vibe.
Now I totally realize that Marcone gets supernatural and criminal street cred for "using" Dresden to destroy his enemies.
And realistically, Harry is not an enemy of Marcone. Harry is, at best, a potential enemy IF and ONLY IF Marcone chooses to go down certain paths. So long as Marcone avoids these paths (ie - dark supernatural stuff or lots of direct harm to innocents), Harry is not going to attack Marcone's interests. And Marcone is not so petty as to resent Harry's strength when it does not come at his expense. Harry can be an accidental threat in that his behavior can create a PR problem for Marcone, but Marcone has proven apt in navigating that hazard.