That's the way VV is for Mac, too (it pauses when you put the window in the background). Not the same for Fish Tycoon, though (I'm selling fish right now
).
You can move the PT window out of the way if you want to read something in the background (push it all the way to the bottom or side), but you can't click out of PT or else it will stop.
I usually just plan to have something else to do away from computer when I sell plants.
As for playing in two windows at the same time, I don't think that's possible in either the Mac or PC versions -- but there are multiple game slots for each window you can switch between, so no need to suck up twice the CPU...
-- jen