for what it's worth, I usually run two windows (in the same frame), side-by-side, with emacs maximised.
On the left I have my org file and on the right I have an R session, which I start immediately after I open my org file.
When I use C-c ' on an R source block, the org buffer (on the left) is replaced by by the source code edit buffer - leaving the R-session on the right untouched.
That way I can either evaluate a whole code block (from org using C-c C-c) or go through the source code line-by-line (using ESS).
Seems like that's what you want to do, too.
Anyway, just my two cents worth, in case it helps.