I'm still not sure about RJ's identity, nonetheless, I have a theory concerning him and TT. 

First, I do believe Bertram is the head (or one of the heads) of Blake Association. HOWEVER, I don't think he is working for RJ, I think he rather wants him eliminated because RJ is causing some trouble on the inside of the Association. My theory is, most of RJ's followers (Craig and Todd for example) were part of Blake Association at first, before they met RJ. Then, he turned them after finding a way for them to work for him. So basically, he "steels" Blake Association members and turns them so HE could be the one controlling them. It makes RJ part of the Association as well. 
The fact that RJ is taking control pisses Bertram off, which is why he's constantly asking Jane some heads up on the RJ case.  He wants him eliminated for good. Everytime he tells Jane "I want to be there where you finish this", you can actually feel that he means every word. He wants to see RJ die once and for all.