If the subconscious motivates actions in a way that we are not aware of, then its fair to say that we don't have control over our subconscious. If I were to look at this from a determinist perspective, than I would say that we don't have any control over any of our actions. Does this mean determinists cant differentiate between actions motivated by the subconscious versus actions motivated by conscious thought?
I do have some conscious control over my subconscious mind. Sometimes I will consider a problem consciously and then let it go and hope for an answer to bubble up from the subconscious. I can consciously change my thinking to change my feelings and hence reactions. Conversely, most of my conscious actions are affected by my subconscious mind. It's not simple at all.
From a deterministic point of view, I don't have free control over my actions. I have conscious control over a good many actions, but if determinism is true it isn't through free will. Still, we have tools now to examine, to some extent, how much the subconscious affects decisions, and that applies whether free will exist or not.