You, my friend, are in dire need of a multiple screen utility. Ultramon may be your best bet:
http://www.realtimesoft.com/ultramon/overview/
That will most probably solve most of your problems. You can add shortcut keys to control window settings quickly, change the primary/secondary screen on the fly, switch applications from one screen to the other, etcetera.
I know it is shareware- give the trial a whirl, and see if this works for you.
edit Since I am working on two screens as well, I tested this with Photoshop - works VERY well: I set up a shortcut key (ctrl-alt-shift-numpad+) to switch any active window to the other screen and vice versa. So when I open a filter window in Photoshop I can now quickly move this dialog to either screen with a flick of my hands. The only thing I noticed is that Photoshop becomes a bit confused when switching from the 22" 16001200 screen to my 19201200 24" screen (the palettes do not move to the far right). However, setting up a shortcut key for maximizing/minimizing the app window and refreshing it (press the key twice) took care of that problem. So now I can switch Photoshop, or any other app, quickly between screens within a second. No more dragging! What’s better, Ultramon takes care of memorizing where the windows are supposed to be going.
edit 2 non-docked palettes stay where they are, and do not move to the other screen.
Combine this with Launchy, and you increase your productivity twice-fold.
http://launchy.net/