I know this has already been suggested before, and as it was suggested, I didn't like it. I personally like how flashfxp will only connect to two sites, but if you've got 10 Flashfxp's open, it can get kind of cluttery.
Would there be any chance of you implementing it in a way like tabbed browsing for web browsers?
Like you have your menu bar, then maybe a bar for selecting from your multiple 2-paned FXP/Download/Upload sessions, then the then icon bar, then your 2-paned selected session?
As I'm sure that is confusing, here is an illustration of the proposal I am making:
