I am also planning to install a Rocket Mass into my greenhouse. I think it is a great idea for growing through the winter because of the slow but constant heat with little wood use. That being said I haven't seen many good examples of functioning greenhouse units with explanations of the effectiveness of heating.
I have read that having cob directly in contact with the stove pipe is good because it will allow the quickest and most complete heat transfer from the pipe, but I've seen plenty that don't do this. I can imagine that if you then had that pipe in a raised bed it would heat the soil which would act as a sufficient thermal mass. Also, the heat is right in the root zone and just above the soil, so if the greenhouse air is cool the plants will still be fine. Here's a video doing that: http://www.youtube.com/watch?v=qtFvdMk3eLM
As far as depth I don't know what the minimum is but I would definitely play it safe, whatever that means... Maybe build a test before you do the final.
Something to consider is how much of the barrel you leave open to the air. I am contemplating how to best eliminate the loss of heat off of my barrel so that I can store the most heat in the thermal mass. This is something you might want to consider if you are only growing winter crops in the winter. I think it would be a better use of the heat to warm your soil not the air (another trick would be to place row cover over the plants to hold in the radiant heat from the soil). I am imagining covering most of the barrel in cob and also increasing the space between the inner chimney and the barrel so that less heat is lost from the barrel top.
As far as putting the heater on the top or bottom of your greenhouse I don't really understand your orientation. I am going to put mine on the ground along the back wall of my greenhouse so that the thermal mass gets lots of sunlight too. However, we are focusing on the production of spring starts for or farm and not on winter growing so our thermal mass is going to be a 3.5' tall cob bench that the starts can sit on.
I think cold sinks are rarely a bad idea, especially after reading Mike Oehlers book. But, I'm not going to do one because of my high water table.
If you haven't, read the Rocket Mass Heaters book by Ianto Evans and Leslie Jackson.