I've found that running the game produces a "default-1.xml" file which looks to be a config file in that it has a line that sets the screen resolution. This site,
http://sglnx.com/tag/graphics/ , though kind of old, suggests renaming it usersettings.xml and placing it in the /preferences/ directory under the main install directory, but there wasn't any preferences folder. I made a prefences folder, copied default-1.xml into it, and changed the screen resolution to 1024*768, set bits to 16, set fbuffer and full to 0, set vsync and darkbuffer to 1, and set darkbuffersize to 256. I set these values in /aquaria/preferences/usersettings.xml , /aquaria/usersettings.xml , and /aquaria/default-1.xml as a kind of blanket solution, since I wasn't sure which one was being read (it's the only way to be sure).
Still, though, the game seems to be trying to startup in fullscreen mode. I hear some nice audio when I run ./aquaria from the install folder, but still the video signal is out of range for my monitor. I would have thought that changing one of those config files would have made the game run in windowed mode at least.
something that may or may not be an issue is that I've installed the game to the /usr/games/ directory. The OS requires you to have root priveledges to mess around in this folder, but I've set the priveledges on the config files to allow read write and even execute permissions for anyone, but that hasn't made any difference, so I'll be pulling execute permissions off.
Still not sure what the issue is here, or why the game won't run in windowed mode.