I typically keep Toolspace, Properties, SSM, Layer Manager, and XREF Manager docked to the left side of my monitor, and set to auto-hide. I don't like to constantly open and close them (although Toolspace often disappears for no apparant reason, and I have to reopen it).
So when I get the "switch", I just switch back to the other drawing, using the "Quick View Drawings" setting in the Status Bar. It's annoying, but not as annoying as constantly opening and closing the Palettes that I use the most.
I run dual monitors and keep toolspace, tool pallet docked to the left and porperties, sheetset manager, xref docked on my second screen along with the layer maager. All of them are minimized to an icon or bar. After reading a post about different bars causing the active drawing to be swapped around I decided to close all my windows. I use 2 instances of civil 3d at a time and usually have at least 3 drawings open. I have not had a problem with my active drawing swapping around. I think it comes down to a personal decision. The convenience of having my windows active but auto-hidden or the annoyance of the active drawing changing. Oh and with the windows closed civil 3d responds much faster which makes sence.