[themaster]

I would say she is probably showing you dominance as she seems to have adopted a protective role that should be yours. The territorial marking would seem to suggets this also, don't allow her to mark, one pee break per walk, when you tell her she can.

If you are in control on the walk your Rott should be responding to what you want her to do and not doing her own thing. Correct any behaviour that you don't want as soon as it starts

I think you are right to be using the choke chain as long as you use it correctly, it sounds like you have her straining and pulling on it and this apart from being dangerous to her will make he pullling and aggression worse.

Give the correction and then treat when you get the desired response, I doubt you will have much success with using treats alone to distract as once the treat is gone she will likely return to the aggression.

You need to get into those training classes as soon as possible.