Scrivener has just the right amount of windows. There’s a place for whatever kind of idea or text you have at hand. Some of these have windows to themselves (scratchpad) and some have multiple views (keywords). I suggest a window like that for keywords for footnotes and comments so that they can be viewed at the same time.
Scrivener has changed my writing world!
On the Mac, you can view all inspector comments and footnotes together by loading your complete manuscript as a Scrivenings session. This isn’t yet doable on Windows, due to the underlying way documents have to be loaded in Scrivenings (so you can only view the comments and footnotes for each individual document as you scroll through the session), but it should be coming as part of an overhaul of that code for 2.0.