Have another window open before you start Aquaria, and then Alt-Tab to the other window. Unmaximize the window (if it is maximized) so that you could see Aquaria's window. Then without going into Aquaria's window frame (the part that you see the game graphics from), drag the title bar to where you want the window to be. It can be tricky sometimes, but they don't have a mouse release key (hint hint, for the open-source developers).